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Boston College
1.
Busby, Michele Anne.
Measuring Gene Expression With Next Generation Sequencing
Technology.
Degree: PhD, Biology, 2012, Boston College
URL: http://dlib.bc.edu/islandora/object/bc-ir:101179 
► While a PhD student in Dr. Gabor Marth's laboratory, I have had primary responsibility for two projects focused on using RNA-Seq to measure differential gene…
(more)
▼ While a PhD student in Dr. Gabor Marth's laboratory, I
have had primary responsibility for two projects focused on using
RNA-
Seq to measure differential gene expression. In the first
project we used
RNA-
Seq to identify differentially expressed genes
in four yeast species and I analyzed the findings in terms of the
evolution of gene expression. In this experiment, gene expression
was measured using two biological replicates of each species of
yeast. While we had several interesting biological findings, during
the analysis we dealt with several statistical issues that were
caused by the experiment's low number of replicates. The cost of
sequencing has decreased rapidly since this experiment's design and
many of these statistical issues can now practically be avoided by
sequencing a greater number of samples. However, there is little
guidance in the literature as to how to intelligently design an
RNA-
Seq experiment in terms of the number of replicates that are
required and how deeply each replicate must be sequenced. My second
project, therefore, was to develop Scotty, a web-based program that
allows users to perform power analysis for
RNA-
Seq experiments. The
yeast project resulted in a highly accessed first author
publication in BMC Genomics in 2011. I have structured my
dissertation as follows: The first chapter, entitled General Issues
in
RNA-
Seq, is intended to synthesize the themes and issues of
RNA-
Seq statistical analysis that were common to both papers. In
this section, I have discussed the main findings from the two
papers as they relate to analyzing
RNA-
Seq data. Like the Scotty
application, this section is designed to be "used" by wet-lab
biologists who have a limited background in statistics. While some
background in statistics would be required to fully understand the
following chapters, the essence of this background can be gained by
reading this first chapter. The second and third chapters contain
the two papers that resulted from the two
RNA-
Seq projects. Each
chapter contains both the original manuscript and original
supplementary methods and data section. Finally, I include brief
summaries of my contributions to the two papers on which I was a
middle author. The first was a functional analysis of the genomic
regions affected by mobile element insertions as a part of Chip
Stewart's paper with the 1000 Genome Consortium. This paper was
published in Plos Genetics. The second was a cluster analysis of
microarray gene expression in Toxoplasma gondii, which was included
as part of Alexander Lorestani et al.'s paper, Targeted proteomic
dissection of Toxoplasma cytoskeleton sub-compartments using MORN1.
This paper is currently under review. The yeast project was a
collaborative effort between Jesse Gray, Michael Springer, and
Allen Costa at Harvard Medical School, Jeffery Chuang here at
Boston College, and members of the Marth lab. Jesse Gray conceived
of the project. While I wrote the draft for the manuscript, many
people, particularly Gabor Marth, provided substantial guidance on
the actual text. I…
Advisors/Committee Members: Gabor Marth (Thesis advisor).
Subjects/Keywords: RNA-Seq
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APA (6th Edition):
Busby, M. A. (2012). Measuring Gene Expression With Next Generation Sequencing
Technology. (Doctoral Dissertation). Boston College. Retrieved from http://dlib.bc.edu/islandora/object/bc-ir:101179
Chicago Manual of Style (16th Edition):
Busby, Michele Anne. “Measuring Gene Expression With Next Generation Sequencing
Technology.” 2012. Doctoral Dissertation, Boston College. Accessed January 22, 2021.
http://dlib.bc.edu/islandora/object/bc-ir:101179.
MLA Handbook (7th Edition):
Busby, Michele Anne. “Measuring Gene Expression With Next Generation Sequencing
Technology.” 2012. Web. 22 Jan 2021.
Vancouver:
Busby MA. Measuring Gene Expression With Next Generation Sequencing
Technology. [Internet] [Doctoral dissertation]. Boston College; 2012. [cited 2021 Jan 22].
Available from: http://dlib.bc.edu/islandora/object/bc-ir:101179.
Council of Science Editors:
Busby MA. Measuring Gene Expression With Next Generation Sequencing
Technology. [Doctoral Dissertation]. Boston College; 2012. Available from: http://dlib.bc.edu/islandora/object/bc-ir:101179
University of Manchester
2.
Lia, Andrei-Stefan.
An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses.
Degree: 2015, University of Manchester
URL: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316
► ABSTRACTThe University of ManchesterAndrei-Stefan LiaMaster of PhilosophyAn RNA-Seq approach to investigate light-controlled gene expression in Neurospora crassa with emphasis on red light-mediated responses14th of October…
(more)
▼ ABSTRACTThe University of ManchesterAndrei-Stefan
LiaMaster of PhilosophyAn
RNA-
Seq approach to investigate
light-controlled gene expression in Neurospora crassa with emphasis
on red light-mediated responses14th of October 2014With increasing
numbers of genomes being sequenced, many phytochrome homologues
have been identified across cyanobacteria, eubacteria and
filamentous fungi. In recent years, two phytochrome homologues were
identified in the filamentous fungus Neurospora crassa. Although
functional and phenotypic analyses have been successful in other
fungal species, the functional significance of Neurospora
phytochromes remains unknown.In this body of work, we aim to
investigate light-regulated gene expression via an
RNA-
Seq
approach. Bioinformatic analysis of
RNA-
Seq data has not only shown
that there is an independent red light response, but that this
response is also controlled by the two phytochrome genes. Our
analysis also confirms previously established light-regulated
genes. We establish differentially expressed gene sets, from which
we extracted cis-regulatory elements.Finally, we also show that
phytochromes are mediators of a thermal acclimation
response.
Advisors/Committee Members: Heintzen, Christian.
Subjects/Keywords: RNA-Seq; phytochrome
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APA (6th Edition):
Lia, A. (2015). An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses. (Doctoral Dissertation). University of Manchester. Retrieved from http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316
Chicago Manual of Style (16th Edition):
Lia, Andrei-Stefan. “An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses.” 2015. Doctoral Dissertation, University of Manchester. Accessed January 22, 2021.
http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316.
MLA Handbook (7th Edition):
Lia, Andrei-Stefan. “An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses.” 2015. Web. 22 Jan 2021.
Vancouver:
Lia A. An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses. [Internet] [Doctoral dissertation]. University of Manchester; 2015. [cited 2021 Jan 22].
Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316.
Council of Science Editors:
Lia A. An RNA-Seq approach to investigate light-controlled gene
expression in Neurospora crassa with emphasis on red light-mediated
responses. [Doctoral Dissertation]. University of Manchester; 2015. Available from: http://www.manchester.ac.uk/escholar/uk-ac-man-scw:259316
University of Cambridge
3.
Westoby, Jennifer.
Alternative splicing and single-cell RNA-sequencing : a feasibility assessment.
Degree: PhD, 2020, University of Cambridge
URL: https://doi.org/10.17863/CAM.52682
;
https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805945
► We know little about how isoform choice is regulated in individual cells for most spliced genes. In theory, single-cell RNA-sequencing (scRNA-seq) could enable us to…
(more)
▼ We know little about how isoform choice is regulated in individual cells for most spliced genes. In theory, single-cell RNA-sequencing (scRNA-seq) could enable us to investigate isoform choice at cellular resolution. Therefore, scRNA-seq could give insight into the fundamental molecular biology process of how alternative splicing is regulated within cells. However, scRNA-seq is a relatively new technology, and at the start of my PhD it was not clear whether existing bioinformatics approaches would enable accurate splicing analyses. In my PhD I consider what the limitations are when attempting to study alternative splicing using scRNA-seq and what can be done to overcome them. Alternative splicing is commonly analysed using bulk RNA sequencing (bulk RNA-seq) data with isoform quantification software. It was not clear whether isoform quantification software designed for bulk RNA-seq would perform well when run on scRNA-seq data. To address this, I performed a simulation-based benchmark of isoform quantification software developed for bulk RNA-seq when run on scRNA-seq. I made two important findings. Firstly, I found that isoform quantification software performs poorly when run on Drop-seq data, but performs better when run on scRNA-seq data generated using full-length transcript protocols (eg. SMART-seq and SMART-seq2). Secondly, I found that for the most part, isoform quantification software performs almost as well when run on full-length scRNA-seq as it does when run on bulk RNA-seq. Based on these findings, I concluded that software tools to accurately quantify the reads from full-length scRNA-seq experiments exist, theoretically enabling alternative splicing to be analysed using scRNA-seq. Encouraged by this result, I embarked on a series of experiments designed to answer questions such as ‘How many isoforms does a gene typically produce per cell?’. This is a key basic biology question that could in theory be answered using scRNA-seq. Unfortunately, I found that the results of these experiments were largely impossible to interpret because I was unable to distinguish between biological signal and technical noise. I realised that without a solid understanding of the technical noise and confounding factors associated with scRNA-seq, distinguishing biological signal from technical noise would be challenging and might not be possible. To address this, I embarked on a second simulation-based study, this time investigating the impact of technical noise on our ability to study alternative splicing using scRNA-seq. I simulated four situations: a situation where every gene expressed one isoform per cell, a situation where all genes expressed two isoforms per cell, a situation where all genes expressed three isoforms per cell and a situation where all genes expressed four isoforms per cell. Importantly, I explicitly simulated isoform choice, dropouts and quantification errors. The results of the four simulated situations were not trivial to distinguish from each other, raising concerns about the feasibility of resolving the…
Subjects/Keywords: splicing; single cell; RNA-seq; scRNA-seq
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APA ·
Chicago ·
MLA ·
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CSE |
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Manager
APA (6th Edition):
Westoby, J. (2020). Alternative splicing and single-cell RNA-sequencing : a feasibility assessment. (Doctoral Dissertation). University of Cambridge. Retrieved from https://doi.org/10.17863/CAM.52682 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805945
Chicago Manual of Style (16th Edition):
Westoby, Jennifer. “Alternative splicing and single-cell RNA-sequencing : a feasibility assessment.” 2020. Doctoral Dissertation, University of Cambridge. Accessed January 22, 2021.
https://doi.org/10.17863/CAM.52682 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805945.
MLA Handbook (7th Edition):
Westoby, Jennifer. “Alternative splicing and single-cell RNA-sequencing : a feasibility assessment.” 2020. Web. 22 Jan 2021.
Vancouver:
Westoby J. Alternative splicing and single-cell RNA-sequencing : a feasibility assessment. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Jan 22].
Available from: https://doi.org/10.17863/CAM.52682 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805945.
Council of Science Editors:
Westoby J. Alternative splicing and single-cell RNA-sequencing : a feasibility assessment. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://doi.org/10.17863/CAM.52682 ; https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.805945
University of Cambridge
4.
Westoby, Jennifer.
Alternative splicing and single-cell RNA-sequencing: a feasibility assessment.
Degree: PhD, 2020, University of Cambridge
URL: https://www.repository.cam.ac.uk/handle/1810/305605
► We know little about how isoform choice is regulated in individual cells for most spliced genes. In theory, single-cell RNA-sequencing (scRNA-seq) could enable us to…
(more)
▼ We know little about how isoform choice is regulated in individual cells for most spliced genes. In theory, single-cell RNA-sequencing (scRNA-seq) could enable us to investigate isoform choice at cellular resolution. Therefore, scRNA-seq could give insight into the fundamental molecular biology process of how alternative splicing is regulated within cells. However, scRNA-seq is a relatively new technology, and at the start of my PhD it was not clear whether existing bioinformatics approaches would enable accurate splicing analyses. In my PhD I consider what the limitations are when attempting to study alternative splicing using scRNA-seq and what can be done to overcome them. Alternative splicing is commonly analysed using bulk RNA sequencing (bulk RNA-seq) data with isoform quantification software. It was not clear whether isoform quantification software designed for bulk RNA-seq would perform well when run on scRNA-seq data. To address this, I performed a simulation-based benchmark of isoform quantification software developed for bulk RNA-seq when run on scRNA-seq. I made two important findings. Firstly, I found that isoform quantification software performs poorly when run on Drop-seq data, but performs better when run on scRNA-seq data generated using full-length transcript protocols (eg. SMART-seq and SMART-seq2). Secondly, I found that for the most part, isoform quantification software performs almost as well when run on full-length scRNA-seq as it does when run on bulk RNA-seq. Based on these findings, I concluded that software tools to accurately quantify the reads from full-length scRNA-seq experiments exist, theoretically enabling alternative splicing to be analysed using scRNA-seq. Encouraged by this result, I embarked on a series of experiments designed to answer questions such as ‘How many isoforms does a gene typically produce per cell?’. This is a key basic biology question that could in theory be answered using scRNA-seq. Unfortunately, I found that the results of these experiments were largely impossible to interpret because I was unable to distinguish between biological signal and technical noise. I realised that without a solid understanding of the technical noise and confounding factors associated with scRNA-seq, distinguishing biological signal from technical noise would be challenging and might not be possible. To address this, I embarked on a second simulation-based study, this time investigating the impact of technical noise on our ability to study alternative splicing using scRNA-seq. I simulated four situations: a situation where every gene expressed one isoform per cell, a situation where all genes expressed two isoforms per cell, a situation where all genes expressed three isoforms per cell and a situation where all genes expressed four isoforms per cell. Importantly, I explicitly simulated isoform choice, dropouts and quantification errors. The results of the four simulated situations were not trivial to distinguish from each other, raising concerns about the feasibility of resolving the…
Subjects/Keywords: splicing; single cell; RNA-seq; scRNA-seq
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APA ·
Chicago ·
MLA ·
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CSE |
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Manager
APA (6th Edition):
Westoby, J. (2020). Alternative splicing and single-cell RNA-sequencing: a feasibility assessment. (Doctoral Dissertation). University of Cambridge. Retrieved from https://www.repository.cam.ac.uk/handle/1810/305605
Chicago Manual of Style (16th Edition):
Westoby, Jennifer. “Alternative splicing and single-cell RNA-sequencing: a feasibility assessment.” 2020. Doctoral Dissertation, University of Cambridge. Accessed January 22, 2021.
https://www.repository.cam.ac.uk/handle/1810/305605.
MLA Handbook (7th Edition):
Westoby, Jennifer. “Alternative splicing and single-cell RNA-sequencing: a feasibility assessment.” 2020. Web. 22 Jan 2021.
Vancouver:
Westoby J. Alternative splicing and single-cell RNA-sequencing: a feasibility assessment. [Internet] [Doctoral dissertation]. University of Cambridge; 2020. [cited 2021 Jan 22].
Available from: https://www.repository.cam.ac.uk/handle/1810/305605.
Council of Science Editors:
Westoby J. Alternative splicing and single-cell RNA-sequencing: a feasibility assessment. [Doctoral Dissertation]. University of Cambridge; 2020. Available from: https://www.repository.cam.ac.uk/handle/1810/305605
5.
Frazee, Alyssa Christine.
High-resolution gene expression analysis.
Degree: 2015, Johns Hopkins University
URL: http://jhir.library.jhu.edu/handle/1774.2/37934
► RNA sequencing (RNA-seq) measures gene expression in cell populations at an unprecedented resolution. The advent of this new technology around 2008 spurred the need for…
(more)
▼ RNA sequencing (
RNA-
seq) measures gene expression in cell populations at an unprecedented resolution. The advent of this new technology around 2008 spurred the need for new techniques for finding scientific meaning in the resulting data. Early statistical techniques for analyzing
RNA-
seq data were inspired by methods for microarray data analysis, and they involved quantifying gene expression by counting the
RNA-
seq reads falling within boundaries of pre-specified genes. However,
RNA-
seq data is very high-resolution, and much of that resolution is lost during the gene counting process. To that end, this thesis introduces novel statistical methods and software for analyzing
RNA-
seq data at a resolution beyond that of gene counting. First, we propose a technique for segmenting the genome into regions of differential expression between two population using single-base-level measures of signal. Next we focus on transcript-level differential expression analysis; in
particular, we introduce tools for finding statistical differential expression signal in transcriptomes that were assembled de novo from
RNA-
seq reads. Finally, we create a tool for evaluating the statistical properties of
RNA-
seq differential expression methods: our new tool generates
RNA-
seq reads to simulate an experiment with known transcript-level differential expression. These statistical and computational contributions to the
RNA-
seq analysis literature further our ability to draw meaningful biological conclusions from high-throughput
RNA sequencing data.
Advisors/Committee Members: Salzberg, Steven L (advisor).
Subjects/Keywords: RNA-seq;
differential expression
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APA (6th Edition):
Frazee, A. C. (2015). High-resolution gene expression analysis. (Thesis). Johns Hopkins University. Retrieved from http://jhir.library.jhu.edu/handle/1774.2/37934
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Frazee, Alyssa Christine. “High-resolution gene expression analysis.” 2015. Thesis, Johns Hopkins University. Accessed January 22, 2021.
http://jhir.library.jhu.edu/handle/1774.2/37934.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Frazee, Alyssa Christine. “High-resolution gene expression analysis.” 2015. Web. 22 Jan 2021.
Vancouver:
Frazee AC. High-resolution gene expression analysis. [Internet] [Thesis]. Johns Hopkins University; 2015. [cited 2021 Jan 22].
Available from: http://jhir.library.jhu.edu/handle/1774.2/37934.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Frazee AC. High-resolution gene expression analysis. [Thesis]. Johns Hopkins University; 2015. Available from: http://jhir.library.jhu.edu/handle/1774.2/37934
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Cornell University
6.
Villarino Pizarro, Gonzalo.
Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.
Degree: PhD, Horticultural Biology, 2014, Cornell University
URL: http://hdl.handle.net/1813/38983
► Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal…
(more)
▼ Abiotic stresses, such as salinity and drought, are among the most limiting factors to crop yield. In sodic saline soils, sodium chloride (NaCl) disrupts normal plant growth and development. Many studies have used both forward and reverse genetic techniques to understand the complex interactions of plant systems with abiotic stress. These approaches have been invaluable in deciphering some mechanisms of plant salt stress tolerance. Salt tolerance research has also been an important part of basic plant biology, increasing the understanding in areas encompassing gene regulation, mineral nutrition, signaling components, ion transport and osmoregulation. To better understand the detrimental effects of NaCl, as well the fundamental questions associated with salt tolerance, transcript regulation in response to NaCl stress was undertaken using ultra-high-throughput
RNA sequencing technology (
RNA-
seq).
RNA-
seq has quickly become the method of choice to perform transcriptomic analysis owing to many advantages over existing platforms. The transcriptomic research presented here was carried out in Petunia hybrida, a salt resistant Solanaceous plant that has also been an excellent model species in molecular genetic research regarding flower development and senescence, synthesis and regulation of volatiles, and so on. In chapter one, to bypass the absence of an available Petunia genome, a de-novo assembled Petunia transcriptome was reconstructed by assembling over one- hundred million Illumina cDNA reads with Trinity software. The de-novo assembled contigs represents the most in-depth transcriptome ever reported for a Petunia species, which can be used as an excellent tool for biological and bioinformatics in the absence of an available Petunia genome. The transcriptome has been made publically available on the SOL Genomics Network (SGN) http://solgenomics.net. Using this newly assembled reference transcriptome, more than 7,000 differentially expressed genes were identified within 24 h of acute NaCl stress. Genes related to regulation of reactive oxygen species, transport, and signal transduction as well as novel and undescribed transcripts were among those differentially expressed in response to salt stress. Gene ontology analyses revealed that plants by 24 h after acute NaCl undertook many changes occurring at the molecular level including genotoxicity, affecting transport and organelles due to the high concentration of Na+ ions.
RNA-
seq, despite the many advantages it offers, it is a relatively new methodology with developments and improvements to be made. At the end of chapter one a modification to the library preparation protocol is presented whereby cDNA samples were bar-coded with non-HPLC purified primers, without affecting the quality and quantity of the
RNA-
seq data. This methodological improvement could substantially reduce the cost of sample preparation for future high-throughput
RNA sequencing experiments. In chapter two, root and leaf transcriptomic response to salt stress was investigated, utilizing the Petunia…
Advisors/Committee Members: Mattson, Neil S. (chair), Mattson, Neil S. (chair), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member), Hanson, Maureen R (committee member), Scanlon, Michael J. (committee member), Nero, Debra (committee member).
Subjects/Keywords: transcriptomics; RNA-seq; Salt stress
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APA (6th Edition):
Villarino Pizarro, G. (2014). Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/38983
Chicago Manual of Style (16th Edition):
Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Doctoral Dissertation, Cornell University. Accessed January 22, 2021.
http://hdl.handle.net/1813/38983.
MLA Handbook (7th Edition):
Villarino Pizarro, Gonzalo. “Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress.” 2014. Web. 22 Jan 2021.
Vancouver:
Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Internet] [Doctoral dissertation]. Cornell University; 2014. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/1813/38983.
Council of Science Editors:
Villarino Pizarro G. Transcriptomic Analysis Of Petunia Hybrida In Response To Salt Stress. [Doctoral Dissertation]. Cornell University; 2014. Available from: http://hdl.handle.net/1813/38983
McMaster University
7.
Gu, Chu-Shu.
A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.
Degree: PhD, 2016, McMaster University
URL: http://hdl.handle.net/11375/20257
► In recent years, the RNA-sequencing (RNA-seq) method, which measures the transcriptome by counting short sequencing reads obtained by high-throughput sequencing, is replacing the microarray technology…
(more)
▼ In recent years, the RNA-sequencing (RNA-seq) method, which measures the transcriptome by counting short sequencing reads obtained by high-throughput sequencing, is replacing the microarray technology as the major platform in gene expression studies. The large amount of discrete data in RNA-seq experiments calls for effective analysis methods. In this dissertation, a new method to detect differentially expressed genes based on quasi-likelihood theory is developed in experiments with a completely randomized design with two experimental conditions. The proposed method estimates the variance function empirically and consequently it has similar sensitivities and FDRs across distributions with different variance functions. In a simulation study, the method is shown to have similar sensitivities and FDRs across the data with three different types of variance functions compared with some other popular methods. This method is applied to a real dataset with two experimental conditions along with some competing methods.
The new method is then extended to more complex designs such as an experiment with multiple experimental conditions, an experiment with block design and an experiment with factorial design. The same advantages for the new method have been found in simulation studies. This method and some competing methods are applied to three real datasets with complex designs.
The new method is also applied to analyze reads per kilobase per million mapped reads (RPKM) data. In the simulation, the method is compared with the Linear Models for Microarray Data (LIMMA) originally developed for microarray analysis (Smyth, 2004) and the question of normalization is also examined. It is shown that the new method and the LIMMA method have similar performance. Further normalization is required for the proper analysis of the RPKM data and the best such normalization is the scaling method. Analyzing raw count data properly has better performance than analyzing the RPKM data. Different normalization and statistical methods are applied to a real dataset with varied gene length across samples.
Thesis
Doctor of Philosophy (PhD)
Advisors/Committee Members: Canty, Angelo, Clinical Epidemiology/Clinical Epidemiology & Biostatistics.
Subjects/Keywords: RNA-seq; Quasi-likelihood; RPKM
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APA (6th Edition):
Gu, C. (2016). A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. (Doctoral Dissertation). McMaster University. Retrieved from http://hdl.handle.net/11375/20257
Chicago Manual of Style (16th Edition):
Gu, Chu-Shu. “A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.” 2016. Doctoral Dissertation, McMaster University. Accessed January 22, 2021.
http://hdl.handle.net/11375/20257.
MLA Handbook (7th Edition):
Gu, Chu-Shu. “A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA.” 2016. Web. 22 Jan 2021.
Vancouver:
Gu C. A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. [Internet] [Doctoral dissertation]. McMaster University; 2016. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/11375/20257.
Council of Science Editors:
Gu C. A QUASI-LIKELIHOOD METHOD TO DETECT DIFFERENTIALLY EXPRESSED GENES IN RNA-SEQUENCE DATA. [Doctoral Dissertation]. McMaster University; 2016. Available from: http://hdl.handle.net/11375/20257
8.
野口, 淳.
mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ.
Degree: Nara Institute of Science and Technology / 奈良先端科学技術大学院大学
URL: http://hdl.handle.net/10061/12488
Subjects/Keywords: RNA-seq
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Manager
APA (6th Edition):
野口, . (n.d.). mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ. (Thesis). Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Retrieved from http://hdl.handle.net/10061/12488
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
野口, 淳. “mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ.” Thesis, Nara Institute of Science and Technology / 奈良先端科学技術大学院大学. Accessed January 22, 2021.
http://hdl.handle.net/10061/12488.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
野口, 淳. “mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ.” Web. 22 Jan 2021.
Note: this citation may be lacking information needed for this citation format:
No year of publication.
Vancouver:
野口 . mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ. [Internet] [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; [cited 2021 Jan 22].
Available from: http://hdl.handle.net/10061/12488.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
Council of Science Editors:
野口 . mRNA-seqを用いたPapaver somniferumの遺伝子発現解析 : Gene expression analysis of Papaver somniferum using mRNA-seq; mRNA-seq オ モチイタ Papaver somniferum ノ イデンシ ハツゲン カイセキ. [Thesis]. Nara Institute of Science and Technology / 奈良先端科学技術大学院大学; Available from: http://hdl.handle.net/10061/12488
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
No year of publication.
University of Notre Dame
9.
Sheri A. Sanders.
Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>.
Degree: Biological Sciences, 2016, University of Notre Dame
URL: https://curate.nd.edu/show/x633dz03m7r
► Amphibians are declining worldwide, in part due to Batrachochytridium dendrobatidis (Bd), a pandemic chytrid fungal disease. This disease affects salamanders more than initially thought,…
(more)
▼ Amphibians are declining worldwide, in part
due to Batrachochytridium dendrobatidis
(Bd), a pandemic chytrid fungal disease. This
disease affects salamanders more than initially thought, but
several gaps in knowledge hinder response to this and other disease
threats. Current demographic information for salamanders is
lacking. Without an efficient means of surveying salamander
populations, it is difficult to monitor or respond to these
declines. Additionally, little is known about how salamanders
respond to chytrid fungus, a major contributor to amphibian
decline. This is particularly worrisome in the Great Lakes Region,
as it is home to a cryptic polyploid complex that makes up the
majority of many salamander communities. These polyploids may be
particularly susceptible to disease, but little is known about
vertebrate response to polyploidy. In this
doctoral dissertation, I address these gaps in salamander
conservation. First I developed eDNA markers that allows for quick,
non-invasive identification of laboratory and field samples without
the need for technical or taxonomic expertise. I used this method
to identify cryptic polyploid and diploid salamanders of the genus
Ambystoma. These salamanders were used in a
transcriptomic study on the functional response of salamanders to
Bd. I was able to sequence, assemble, annotate,
and analyze three salamander transcriptomes using this data. I
characterized the immune response of one of these salamanders to
Bd, finding links to wound healing pathways
characteristic of salamanders and generally much quicker response
time to chytrid challenge than is observed in frogs. Additionally,
I investigated the expression patterns of polyploid salamanders in
comparison to the parental taxa in normal and disease conditions. I
found that different genomic copies within the polyploids maintain
their own regulation patterns under normal conditions, but are
disrupted in disease conditions. This may indicate an increase
susceptibility to chytrid in the highly common salamander
polyploids and other vertebrate polyploids. What
follows are an introductory chapter, three data chapters, and a
conclusion where I offer my concluding remarks on the utility of
these chapters and the future importance of such analyses in
conservation genomics, particularly in light of recently discovery
of a more pathogenic chyrid fungus, Batrachochytridium
salamandervorans.
Advisors/Committee Members: Michael Pfrender, Research Director.
Subjects/Keywords: RNA-seq; chytrid; salamander; Ambystoma
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sanders, S. A. (2016). Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/x633dz03m7r
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Sanders, Sheri A.. “Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>.” 2016. Thesis, University of Notre Dame. Accessed January 22, 2021.
https://curate.nd.edu/show/x633dz03m7r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Sanders, Sheri A.. “Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>.” 2016. Web. 22 Jan 2021.
Vancouver:
Sanders SA. Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>. [Internet] [Thesis]. University of Notre Dame; 2016. [cited 2021 Jan 22].
Available from: https://curate.nd.edu/show/x633dz03m7r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Sanders SA. Conservation Transcriptomics of Ambystomatid Salamanders and
Their Polyploid Hybrids</h1>. [Thesis]. University of Notre Dame; 2016. Available from: https://curate.nd.edu/show/x633dz03m7r
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Notre Dame
10.
Kyle Dubiak.
The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>.
Degree: Chemistry and Biochemistry, 2020, University of Notre Dame
URL: https://curate.nd.edu/show/qj72p557p9r
► Xenopus laevis has proven itself as a powerful and indispensable model organism in the field of developmental biology. However, it has begun to spread…
(more)
▼ Xenopus laevis has proven
itself as a powerful and indispensable model organism in the field
of developmental biology. However, it has begun to spread into
other fields of research, one of which being analytical chemistry
and quantitative proteomics. Beginning with the largest
developmental proteome dataset of any organism at that time,
Xenopus laevis has since been utilized in
countless analytical experiments, ranging from single cell
proteomics and metabolomics, protein extraction optimization, and
phosphoproteomics. In this work, I continued integrating numerous
analytical techniques while investigating various developmental
aspects of Xenopus embryology. This has resulted
in furthering single cell proteomic sensitivity, whole embryo
metabolite imaging, N-glycoproteome
quantitation, conduction system analysis of the developing heart,
and the integration of proteomics and transcriptomics investigating
neural cell lineage commitment.
Advisors/Committee Members: Paul W Huber, Research Director.
Subjects/Keywords: RNA-seq; Proteomics; Developmental Biology
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Dubiak, K. (2020). The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>. (Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/qj72p557p9r
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Dubiak, Kyle. “The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>.” 2020. Thesis, University of Notre Dame. Accessed January 22, 2021.
https://curate.nd.edu/show/qj72p557p9r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Dubiak, Kyle. “The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>.” 2020. Web. 22 Jan 2021.
Vancouver:
Dubiak K. The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>. [Internet] [Thesis]. University of Notre Dame; 2020. [cited 2021 Jan 22].
Available from: https://curate.nd.edu/show/qj72p557p9r.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Dubiak K. The Proteomic, Transcriptomic, and Metabolomic Analyses of
Developing Xenopus laevis
Embryos</h1>. [Thesis]. University of Notre Dame; 2020. Available from: https://curate.nd.edu/show/qj72p557p9r
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Minnesota
11.
Gao, Liangliang.
Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.
Degree: PhD, Plant pathology, 2013, University of Minnesota
URL: http://purl.umn.edu/146706
► Wild potato Solanum bulbocastanum is a rich source of genetic resistance against a variety of pathogens. This project developed molecular tools and expanded biological knowledge…
(more)
▼ Wild potato Solanum bulbocastanum is a rich source of genetic resistance against
a variety of pathogens. This project developed molecular tools and expanded biological
knowledge useful for the improvement of cultivated potato (S. tuberosum) using genetic
resistance from S. bulbocastanum. First, the genome structure of S. bulbocastanum
relative to those of its relatives, cultivated potato and tomato (S. lycopersicon) was
determined. Second, to facilitate efforts to improve cultivated potato through the
introgression and deployment disease resistance derived from S. bulbocastanum, the
phenotypic function and molecular mechanisms of one S. bulbocastanum disease
resistance gene were explored in cultivated potato foliage and tubers.
For determination of genome structure for S. bulbocastanum, Diversity Arrays
Technology (DArT) was employed to generate genome wide linkage maps for the
species. Employing a pseudo-testcross mapping strategy, 631 DArT markers were
integrated into a composite map comprising 12 linkage groups. Our results represent an over ten-fold increase of total marker density compared to previously available genetic
maps for the species. Sequencing and alignment of corresponding DArT clones to
reference physical maps from tomato and cultivated potato allowed a direct comparison
of marker orders between species. Overall, the S. bulbocastanum genetic maps show
higher collinearity with reference potato maps than tomato maps, with seven genome
regions supporting a closer phylogenetic relationship between potato and S.
bulbocastanum than between tomato and S. bulbocastanum. One dominant US cultivar ‘Russet Burbank’(WT; late blight susceptible in foliage
and tuber) and its RB (a late blight resistance gene derived from S. bulbocastanum)
transgenic line SP2211 (+RB; late blight resistant in foliage and tuber) were compared in
both tubers and foliage in their responses to late blight pathogen attack using an RNA-seq
approach. In the tubers, a total of 483 million paired end Illumina RNA-seq reads were
generated, representing the transcription of 29,319 potato genes. Differentially expressed
genes, gene groups and ontology bins that exhibited differences between the WT and
+RB lines were identified. P. infestans transcripts, including those of known effectors,
were also identified. Faster and stronger activation of defense related genes, gene groups and ontology bins correlated with successful tuber resistance against P. infestans. Our
results suggest that the hypersensitive response is likely a general form of resistance
against the hemibiotrophic P. infestans—even in potato tubers, organs that develop below
ground.
In the foliage, a total of 515 million paired end RNA-seq reads were generated,
representing the transcription of 29,970 genes. We compared the differences and
similarities of responses to P. infestans in potato foliage and tubers. Differentially
expressed genes, gene groups and ontology bins were identified to show similarities and
differences in foliage and tuber…
Subjects/Keywords: Late blight; Potato; RNA-seq
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Gao, L. (2013). Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. (Doctoral Dissertation). University of Minnesota. Retrieved from http://purl.umn.edu/146706
Chicago Manual of Style (16th Edition):
Gao, Liangliang. “Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.” 2013. Doctoral Dissertation, University of Minnesota. Accessed January 22, 2021.
http://purl.umn.edu/146706.
MLA Handbook (7th Edition):
Gao, Liangliang. “Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage.” 2013. Web. 22 Jan 2021.
Vancouver:
Gao L. Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. [Internet] [Doctoral dissertation]. University of Minnesota; 2013. [cited 2021 Jan 22].
Available from: http://purl.umn.edu/146706.
Council of Science Editors:
Gao L. Generation of genome wide linkage maps for a wild potato and RNA-seq analysis of transgene mediated potato defense mechanisms against late blight in the tubers and foliage. [Doctoral Dissertation]. University of Minnesota; 2013. Available from: http://purl.umn.edu/146706
Louisiana State University
12.
Bedre, Renesh.
Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.
Degree: PhD, 2016, Louisiana State University
URL: etd-07112016-114436
;
https://digitalcommons.lsu.edu/gradschool_dissertations/2251
► Aflatoxins are toxic and potent carcinogenic metabolites produced by Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive environmental conditions. Much success has…
(more)
▼ Aflatoxins are toxic and potent carcinogenic metabolites produced by Aspergillus flavus and A. parasiticus. Aflatoxins can contaminate cottonseed under conducive environmental conditions. Much success has been achieved by the application of atoxigenic strains of A. flavus for controlling aflatoxin contamination in cotton, peanut and maize. Development of aflatoxin-resistant cultivars overexpressing resistance-associated genes and/or knocking down aflatoxin biosynthesis of A. flavus could be an effective strategy for controlling aflatoxin contamination in cotton. In this study, differentially expressed genes (DEGs) were identified in response to infection with both toxigenic and atoxigenic strains of A. flavus pericarp and seed of cotton through genome-wide transcriptome profiling. The genes involved in antifungal response, oxidative burst, transcription factors, defense signaling pathways and stress response were highly differentially expressed in pericarp and seed tissues in response to A. flavus infection. The cell-wall modifying genes and genes involved in the production of antimicrobial substances were more active in pericarp than seed. Genes involved in defense response in cotton were highly induced in pericarp. The DEGs will serve as the source for identifying biomarkers for breeding, potential candidate genes for transgenic manipulation, and will help in understanding complex plant-fungal interaction for future downstream research. The increasing volume of sequence data generated by the rapidly decreasing cost of RNA sequencing (RNA-Seq) necessitates the development of software pipeline(s) that can analyze the massive amounts of RNA-Seq data in an efficient manner. Through the present study, a comprehensive and flexible Standalone RNA-Seq Analysis Pipeline (SRAP) implemented with the parallel programming approach was developed, which can analyze transcriptome for any genome. SRAP consists of high-level modules, including sequence reads filtering, mapping to reference genome (or transcriptome), sequence assembly, gene expression analysis and variant discovery along with low-level modules for other common NGS utilities. The high-level modules, unlike low-level modules, require intense computation in terms of memory and processor. SRAP is developed with in-house developed scripts (Python), parallel computing and open source bioinformatics tools. It can be executed as a batch and/or individual mode for single or multiple sample files. SRAP generates RNA-Seq data analysis output files with statistical summary and graphic visualization.
Subjects/Keywords: NGS; SRAP; Aflatoxins; RNA-Seq
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Bedre, R. (2016). Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251
Chicago Manual of Style (16th Edition):
Bedre, Renesh. “Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.” 2016. Doctoral Dissertation, Louisiana State University. Accessed January 22, 2021.
etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251.
MLA Handbook (7th Edition):
Bedre, Renesh. “Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline.” 2016. Web. 22 Jan 2021.
Vancouver:
Bedre R. Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. [Internet] [Doctoral dissertation]. Louisiana State University; 2016. [cited 2021 Jan 22].
Available from: etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251.
Council of Science Editors:
Bedre R. Genome-wide Transcriptome Analysis of Cotton (Gossypium hirsutum L.) to Identify Genes in Response to Aspergillus flavus Infection, and Development of RNA-Seq Data Analysis Pipeline. [Doctoral Dissertation]. Louisiana State University; 2016. Available from: etd-07112016-114436 ; https://digitalcommons.lsu.edu/gradschool_dissertations/2251
Princeton University
13.
Watson, Colin.
Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
.
Degree: PhD, 2016, Princeton University
URL: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t
► Characterizing Early Zygotic Dosage Compensation in Drosophila melanogaster using RNA-Seq Sexual reproduction in flies, mammals, and worms results in males and females receiving different numbers…
(more)
▼ Characterizing Early Zygotic Dosage Compensation in Drosophila melanogaster using
RNA-
Seq
Sexual reproduction in flies, mammals, and worms results in males and females receiving different numbers of X chromosomes. A chromosome wide regulatory process termed dosage compensation counteracts the differences in X-linked gene expression between sexes by balancing X-chromosome transcript levels. In Drosophila melanogaster, the Dosage Compensation Complex (DCC) forms in the presence of Msl-2 and activates a two-fold increase in gene expression. However multiple questions still remain regarding the function of the DCC as recent studies indicate the presence of an alternative dosage compensation mechanism. Sex lethal (Sxl), an
RNA binding protein involved in sex determination is believed to play a role in this alternative model by regulating X-linked female transcripts. In this study we will examine the mechanism behind early zygotic dosage compensation using a novel high-throughput approach to sort male and female embryos during early embryogenesis. We use
RNA-
Seq to measure zygotic expression levels in male and female embryos. We then characterize Sxl and Msl-1 loss-of-function mutants to determine the mechanism behind early dosage compensation. Our study intends to further our understanding of sex specific transcription on a global scale during early Drosophila development.
Determining Spiroplasma MSRO’s role in Drosophila melanogaster male lethality
Spiroplasma MSRO are maternally transmitted bacteria that infect Drosophila melanogaster and induce apoptosis in male embryos during early embryogenesis. Previous reports have implicated the male dosage compensation complex (DCC) as a factor in male lethality as the loss of any DCC gene suppresses Spiroplasma induced apoptosis. In this study we characterize Spiroplasma’s impact on the male embryo’s molecular and morphogenetic development. We use
RNA-
Seq to measure transcript levels in infected male and female embryos during early embryogenesis. To determine if the loss of the dosage compensation system rescues transcript mis-regulation we quantify gene expression in homozygous Msl-1 embryos. We show that mis-regulation is sex specific and that Drosophila autosomal and X-linked genes are affected. We demonstrate that the loss of DCC functionality rescues transcript mis-regulation in infected male embryos. Our study intends to further our understanding of sex specific host-symbiont interactions.
Advisors/Committee Members: Wieschaus, Eric (advisor).
Subjects/Keywords: Dosage Compensation;
RNA-Seq;
Spiroplasma
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Watson, C. (2016). Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
. (Doctoral Dissertation). Princeton University. Retrieved from http://arks.princeton.edu/ark:/88435/dsp01tb09j815t
Chicago Manual of Style (16th Edition):
Watson, Colin. “Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
.” 2016. Doctoral Dissertation, Princeton University. Accessed January 22, 2021.
http://arks.princeton.edu/ark:/88435/dsp01tb09j815t.
MLA Handbook (7th Edition):
Watson, Colin. “Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
.” 2016. Web. 22 Jan 2021.
Vancouver:
Watson C. Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
. [Internet] [Doctoral dissertation]. Princeton University; 2016. [cited 2021 Jan 22].
Available from: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t.
Council of Science Editors:
Watson C. Dynamics Of Early Zygotic Dosage Compensation and a Characterization of Spiroplasmas Role in Drosophila Male-Killing
. [Doctoral Dissertation]. Princeton University; 2016. Available from: http://arks.princeton.edu/ark:/88435/dsp01tb09j815t
University of New South Wales
14.
Mills, James.
Human brain transcriptomic: towards understanding multiple system atrophy.
Degree: Biotechnology & Biomolecular Sciences, 2015, University of New South Wales
URL: http://handle.unsw.edu.au/1959.4/55473
;
https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
► The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form…
(more)
▼ The human brain is a remarkably complex organ. It is a heterogeneous collection of billions of neurons and glial cells that are interconnected to form a finely tuned network capable of higher cognition. It is thought that the transcriptome may hold the key to understanding the complexity seen in the human brain. Next-generation sequencing allows the brain’s transcriptome to be probed at an unmatched resolution. This has uncovered a myriad of
RNA elements, including
RNA that does not code for protein, known as non-coding
RNA (ncRNA). Originally, thought to be transcriptional noise, it is now appreciated that ncRNAs have numerous functional properties, with the ability to interact with DNA, other
RNA molecules and proteins in different cellular compartments. It is thought that an increase in the number of ncRNAs being expressed throughout the brain, is a major driver of the increased intellectual capacity seen in humans and primates. The increase in the complexity of the human brain, also makes it prone to a number of different neurodegenerative and psychiatric diseases. These diseases are set to have dramatic economic and social impacts by the middle of the 21st century. To avert this looming epidemic an adequate understanding of the human brain is needed, so diagnostic tools and treatment targets can be developed. One such disorder is multiple system atrophy(MSA). MSA is a sporadic, rapidly progressing neurodegenerative disease. Currently no treatment exists and very little is known about the molecular basis of MSA. Before an understanding of the diseased brain can be reached an understanding of the healthy brain is necessary.Here, the transcriptome of grey matter (GM) and white matter (WM) from the superior frontal gyrus (SFG) of the healthy prefrontal cortex (PFC) was analysed. This revealed pervasive transcription and highlighted the differences in the transcriptome profiles of distinct cortical structures throughout the brain. A number of protein-coding genes were expressed exclusively in GM or WM, including gamma-aminobutyric acid A receptor, beta 2 (GABRB2) and P21 Protein (Cdc42/Rac)-Activated Kinase 2 (PAK2), respectively. Further, an interesting phenomenon known as isoform switching was detected in genes such as the G protein-coupled receptor 123 (GPR123). It was also revealed that in the healthy frontal cortex long intervening non-coding RNAs (lincRNAs), a subclass of long non-coding RNAs (lncRNAs), appear to be important drivers of tissue differentiation.To further establish the role of lincRNAs in the healthy human brain a comprehensive analysis of the oligodendrocyte maturation-associated lincRNA (OLMALINC) was carried out. It was found that OLMALINC is a recently evolved lincRNA with its highest expression levels in the human brain. OLMALINC was knocked down in human neurons and oligodendrocytes. Depletion of OLMALINC transcription revealed that it plays a role oligodendrocyte maturation. This study was one of the first functional characterisations of a lincRNA expressed in the human brain, and thus…
Advisors/Committee Members: Janitz, Michael, Faculty of Science, UNSW.
Subjects/Keywords: Neurodegeneration; RNA-Seq; Long non-coding RNA
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Mills, J. (2015). Human brain transcriptomic: towards understanding multiple system atrophy. (Doctoral Dissertation). University of New South Wales. Retrieved from http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
Chicago Manual of Style (16th Edition):
Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Doctoral Dissertation, University of New South Wales. Accessed January 22, 2021.
http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.
MLA Handbook (7th Edition):
Mills, James. “Human brain transcriptomic: towards understanding multiple system atrophy.” 2015. Web. 22 Jan 2021.
Vancouver:
Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Internet] [Doctoral dissertation]. University of New South Wales; 2015. [cited 2021 Jan 22].
Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true.
Council of Science Editors:
Mills J. Human brain transcriptomic: towards understanding multiple system atrophy. [Doctoral Dissertation]. University of New South Wales; 2015. Available from: http://handle.unsw.edu.au/1959.4/55473 ; https://unsworks.unsw.edu.au/fapi/datastream/unsworks:37793/SOURCE02?view=true
University of Newcastle
15.
Geaghan, Michael.
Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA.
Degree: PhD, 2019, University of Newcastle
URL: http://hdl.handle.net/1959.13/1406560
► Research Doctorate - Doctor of Philosophy (PhD)
Schizophrenia is a severely debilitating psychiatric disorder which typically presents as a combination of symptoms including hallucinations, delusions,…
(more)
▼ Research Doctorate - Doctor of Philosophy (PhD)
Schizophrenia is a severely debilitating psychiatric disorder which typically presents as a combination of symptoms including hallucinations, delusions, social withdrawal, and cognitive deficits. While much research to date has investigated various aspects of its pathophysiology and neurobiology, there are still many unknowns. In this thesis I have employed next-generation RNA sequencing technology to investigate the roles of microRNAs (miRNAs) in regulating the post-transcriptional expression profile of cells in schizophrenia. This was accomplished via three studies. In the first study, peripheral blood mononuclear cell (PBMC) samples from healthy controls and individuals with schizophrenia were analysed for changes in both miRNA and gene expression via RNA sequencing analysis. This data revealed an increase in immune-related gene expression among males with schizophrenia. These results were accompanied by reductions in the expression of various miRNAs predicted to target these genes, suggesting that these miRNAs – including miR-1271-5p, miR-221-5p, and let-7a-5p – may be important for regulating peripheral immune activity, and thus may be involved in regulating the abnormal immune activation that has been observed in schizophrenia. In the second study, a cell culture model of elevated DGCR8 expression was employed, using the neuron-like, differentiated SH-SY5Y human neuroblastoma cell line. The elevation of the miRNA biogenesis gene DGCR8 has been observed in brain tissue in schizophrenia and may represent a global change to miRNA biogenesis in neural tissue in the disorder. Analysis of miRNA and mRNA expression in this cell culture model via RNA sequencing revealed wide-sweeping changes to both expression profiles, and in particular demonstrated a reduction in expression of numerous genes involved in neuronal function, as well as genes known to be associated with schizophrenia. Furthermore, various cell cycle and apoptotic genes were upregulated, suggesting these processes could be involved in the disorder as well. Furthermore, the transcription factor YY1 was found to regulate DGCR8, and downregulation of this gene resulted in a similar miRNA expression profile to DGCR8 elevation, adding to preliminary evidence that this transcription factor may also be involved in schizophrenia neurobiology. Finally, the third study investigated the miRNA miR-1271-5p, again using the SH-SY5Y cell culture model. This miRNA was among the differentially expressed miRNAs elevated in the first study of PBMC RNA expression, and our lab has identified it as a potential player in regulating gene expression following neuronal depolarisation. This study involved both overexpressing and knocking down miR-1271-5p in vitro and employed both mRNA sequencing to investigate gene expression changes, as well as ribosome profiling to identify differentially translated genes. The results of this study suggest that this miRNA is involved in both regulating the cell cycle as well as aspects of…
Advisors/Committee Members: University of Newcastle. Faculty of Health & Medicine, School of Biomedical Sciences and Pharmacy.
Subjects/Keywords: RNA; microRNA; miRNA; sequencing; RNA-seq; ribo-seq; gene expression; schizophrenia
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APA (6th Edition):
Geaghan, M. (2019). Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA. (Doctoral Dissertation). University of Newcastle. Retrieved from http://hdl.handle.net/1959.13/1406560
Chicago Manual of Style (16th Edition):
Geaghan, Michael. “Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA.” 2019. Doctoral Dissertation, University of Newcastle. Accessed January 22, 2021.
http://hdl.handle.net/1959.13/1406560.
MLA Handbook (7th Edition):
Geaghan, Michael. “Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA.” 2019. Web. 22 Jan 2021.
Vancouver:
Geaghan M. Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA. [Internet] [Doctoral dissertation]. University of Newcastle; 2019. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/1959.13/1406560.
Council of Science Editors:
Geaghan M. Characterising transcriptional perturbations arising from altered expression of schizophrenia-associated microRNA. [Doctoral Dissertation]. University of Newcastle; 2019. Available from: http://hdl.handle.net/1959.13/1406560
University of Minnesota
16.
Nair, Asha.
A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.
Degree: PhD, Biomedical Informatics and Computational Biology, 2018, University of Minnesota
URL: http://hdl.handle.net/11299/199034
► High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased…
(more)
▼ High-throughput Next Generation RNA sequencing (RNA-Seq) technology is affluent with information about the transcriptome, which includes both protein-coding and multiple non-coding regions. In a diseased state, complex interactions between these regions can go awry. Identification of such interactions is critical to translate the underlying biology of the transcriptome, especially for lethal diseases such as cancer. The field of bioinformatics is currently deficient in workflows that can analyze both coding and non-coding regions together efficiently, to identify disease-specific interactions. In this dissertation, I developed three coherent bioinformatics solutions that aim to address these shortcomings in RNA-Seq. First, a comprehensive workflow called MAPR-Seq was developed to analyze and report various features of protein-coding messenger RNAs. Second, a workflow for non-coding circular RNAs, called Circ-Seq, was developed to identify, quantify and annotate expressed circular RNAs. Third, an integration workflow called ReMIx was developed to identify microRNA response elements (MREs) and integrate them with the different types of RNAs (messenger RNAs, circular RNAs, and microRNAs). Collectively, the three workflows were applied to the largest cohort of breast cancer samples (n=885) from The Cancer Genome Atlas (TCGA). Based on the results obtained from these workflows, I present several key findings that are pertinent to breast cancer. I show that circular RNAs may be a marker for tumor proliferation in estrogen response positive (ER+) breast cancer subtype. I also show how triple negative (TN) breast cancer subtype-specific MRE signatures of messenger RNA – microRNA interactions can be obtained using RNA-Seq data, which has not been explored to date and thus, is a novel undertaking. In the end, my results highlight candidate messenger RNAs, circular RNAs and microRNAs that are found to be associated with MAPK and PI3K/AKT signaling cascades in TN breast cancer subtype. In general, the developed bioinformatics solutions can also be applied to RNA-Seq data of other cancer subtypes and diseases to identify unique messenger RNA – microRNA – circular RNA candidates that could be promising diagnostic targets towards improving treatment options for complex diseases.
Subjects/Keywords: circular RNA; integration; messenger RNA; micro RNA; MRE; RNA-Seq
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APA (6th Edition):
Nair, A. (2018). A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. (Doctoral Dissertation). University of Minnesota. Retrieved from http://hdl.handle.net/11299/199034
Chicago Manual of Style (16th Edition):
Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Doctoral Dissertation, University of Minnesota. Accessed January 22, 2021.
http://hdl.handle.net/11299/199034.
MLA Handbook (7th Edition):
Nair, Asha. “A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs.” 2018. Web. 22 Jan 2021.
Vancouver:
Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Internet] [Doctoral dissertation]. University of Minnesota; 2018. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/11299/199034.
Council of Science Editors:
Nair A. A novel bioinformatics approach to characterize and integrate messenger RNAs, circular RNAs and micro RNAs. [Doctoral Dissertation]. University of Minnesota; 2018. Available from: http://hdl.handle.net/11299/199034
17.
Briaud, Paul.
Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung.
Degree: Docteur es, Microbiologie, 2019, Lyon
URL: http://www.theses.fr/2019LYSE1345
► Les poumons des patients atteints de mucoviscidose (CF) sont séquentiellement colonisés par Staphylococcus aureus puis par Pseudomonas aeruginosa (PA). Lors de cette colonisation, ces deux…
(more)
▼ Les poumons des patients atteints de mucoviscidose (CF) sont séquentiellement colonisés par Staphylococcus aureus puis par Pseudomonas aeruginosa (PA). Lors de cette colonisation, ces deux bactéries interagissent l’une avec l’autre selon deux modes possibles. Une interaction compétitrice, bien caractérisée, est généralement observée dans les co-colonisations précoces où des produits issus du quorum-sensing de PA ralentissent la croissance de SA et entrainent sa lyse. Une interaction de coexistence, peu caractérisée se produit avec les souches dites tardives de PA qui ne sont plus virulentes envers SA. L’objectif de mes travaux de recherche a été de caractériser l’impact de PA sur la physiologie de SA. Des analyses transcriptomiques et confirmations phénotypiques sur des isolats cliniques en coexistence révèlent une amélioration de la résistance aux antibiotiques et de l’internalisation de SA dans les cellules de l’hôte, en présence de PA. Une approche par Tn-seq a identifié des gènes codant de grands régulateurs majeurs de SA (agr, sigB, arlR) comme étant essentiels dans cette interaction de coexistence. Une étude clinique rétrospective menée sur la cohorte lyonnaise des patients CF a montré que 65% des patients co-colonisés présentaient une paire SA-PA en état de coexistence. Cette étude note une détérioration pulmonaire dépendante du statut infectieux (SA<PA=SA+PA). Mon projet a donc montré que la présence des régulateurs globaux de SA sont importants pour coexister avec PA et de modifier son transcriptome augmentant sa résistance aux antibiotiques et son internalisation. Le caractère poly bactérien des infections devrait être pris en compte lors des traitements
Cystic fibrosis (CF) patient lung are colonized by Staphylococcus aureus (SA) and Pseudomonas aeruginosa (PA) in this subsequent order. These bacteria interact each other during this colonization and two different interaction states are often depicted. The well-known competition state occurs when the so-called early infecting strains of PA produce quorum-sensing dependent virulence factors slowing SA growth and leading to its lysis. On the contrary the late-infecting strains of PA are not able to produce these virulence factors and a coexistence state seems to emerge with SA. The aim of my thesis project was to decipher the impact of PA coexisting strains on SA lifestyle. Transcriptomic analyses followed by phenotypic experiments confirmed an increase of SA antibiotic resistance its internalization within host cells, in the presence of PA. A Tn-seq method identified SA genes involved in major regulators (e.g agr system, sigB operon, alrR) as essential for the coexistence state with PA. Moreover, a retrospective clinical study on Lyon CF patient’s cohort showed that 65% of co-infected patients carried a coexisting SA/PA couple of strains. This study also indicated that the infectious status of CF patient was correlated with the severity of the disease (SA<PA=SA+PA). My project concludes about the importance of SA major regulators in this coexistence state…
Advisors/Committee Members: Moreau, Karen (thesis director).
Subjects/Keywords: Mucoviscidose; Interaction; Coexistence; Staphylococcus; Pseudomonas; RNA-seq; TN-seq; Cystic fibrosis; Interaction; Coexistence; Staphylococcus; Pseudomonas; RNA-seq; TN-seq; 570
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Briaud, P. (2019). Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung. (Doctoral Dissertation). Lyon. Retrieved from http://www.theses.fr/2019LYSE1345
Chicago Manual of Style (16th Edition):
Briaud, Paul. “Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung.” 2019. Doctoral Dissertation, Lyon. Accessed January 22, 2021.
http://www.theses.fr/2019LYSE1345.
MLA Handbook (7th Edition):
Briaud, Paul. “Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung.” 2019. Web. 22 Jan 2021.
Vancouver:
Briaud P. Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung. [Internet] [Doctoral dissertation]. Lyon; 2019. [cited 2021 Jan 22].
Available from: http://www.theses.fr/2019LYSE1345.
Council of Science Editors:
Briaud P. Impact de Pseudomonas aeruginosa sur Staphylococcus aureus dans un contexte de coexistence bactérienne chez les patients atteints de mucoviscidose : Impact of Pseudomonas aeruginosa on Staphylococcus aureus in a context of coexistence in cystic fibrosis patient lung. [Doctoral Dissertation]. Lyon; 2019. Available from: http://www.theses.fr/2019LYSE1345
University of California – Santa Cruz
18.
Smith, Andrew Martin.
Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.
Degree: Chemistry, 2017, University of California – Santa Cruz
URL: http://www.escholarship.org/uc/item/24b97646
► This work describes advances in nanopore sequencing technology as they apply to RNA. RNAs in the cellular environment have a wide range of functions and…
(more)
▼ This work describes advances in nanopore sequencing technology as they apply to RNA. RNAs in the cellular environment have a wide range of functions and structures, by nature being much more dynamic in their activities than their chemical counterpart, DNA. The diversity of activities and functions that RNAs assume in the cell is reflected in the diverse research interests of those who study RNA. Any effort to develop nanopore-based direct RNA sequencing applications requires accounting for this diversity.Given the spectrum of interests in RNA biology, much of this dissertation attempts to address a fundamental challenge in directly analyzing RNAs by nanopore - how to deliver and read diverse classes of RNA at single-nucleotide resolution using a nanopore sequencer? The introductory first chapter describes background on nanopores as sequencing sensors and samples of some biology surrounding this diverse class of molecules. The state of the art and challenges in RNA sequencing in general are discussed. The second chapter of this work demonstrates a method specifically preparing tRNA for nanopore sequencing. The primary challenge in this effort is to be able to consistently load a single tRNA end and process the tRNA strand through the pore in a linear order. A molecular adapter composed of double-stranded DNA ligated to the tRNA termini facilitates this process. The adapter specifically targets tRNA by hybridizing to the universally conserved CCA tail of tRNA. It also provides a binding site for ϕ29 DNA polymerase, which acts a molecular brake on RNA under non-catalytic conditions. These two features allow for discrimination between two tRNA species from E. coli. This work demonstrates that it is possible to use a nanopore to analyze individual tRNAs as linear strands, which is a necessary prerequisite for nanopore-based tRNA sequencing.The third chapter of this work describes applying the Oxford Nanopore MinION sequencer to directly sequence 16S ribosomal RNA (16S rRNA). Demonstration of direct RNA sequencing of poly-adenylated RNA by Oxford Nanopore in August of 2016 was a critical development towards direct sequencing of RNA in general. The work described in Chapter 3 again involves designing an adapter, but this time specific for prokaryotic 16S rRNA. This adapter can be used with the existing Oxford Nanopore direct RNA sequencing kit. Sequencing of 16S rRNA from E. coli and other three other microbial species is demonstrated. The data and confirmatory experiments show that it is possible to directly detect modified ribonucleotides in nanopore-based sequencing data, which has long been a promised benefit of direct RNA sequencing methods. The 16S rRNA adapter is designed to hybridize to conserved 3′-end sequence of E. coli 16S rRNA. It could be generalized to all prokaryotic 16S rRNA, which would be desirable for rapid identification of prokaryotic microbes in a clinical or environmental setting.The appendices cover unpublished work on helicase proteins to control RNA strand movement through a nanopore. The…
Subjects/Keywords: Biochemistry; Biophysics; Nanotechnology; epigenetics; nanopore; RNA; RNA-seq; RNA sequencing; tRNA
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APA ·
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APA (6th Edition):
Smith, A. M. (2017). Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/24b97646
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Smith, Andrew Martin. “Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.” 2017. Thesis, University of California – Santa Cruz. Accessed January 22, 2021.
http://www.escholarship.org/uc/item/24b97646.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Smith, Andrew Martin. “Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores.” 2017. Web. 22 Jan 2021.
Vancouver:
Smith AM. Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. [Internet] [Thesis]. University of California – Santa Cruz; 2017. [cited 2021 Jan 22].
Available from: http://www.escholarship.org/uc/item/24b97646.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Smith AM. Principles and Advances in Analysis of Ribonucleic Acid Sequence Using Nanopores. [Thesis]. University of California – Santa Cruz; 2017. Available from: http://www.escholarship.org/uc/item/24b97646
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Santa Cruz
19.
Uzilov, Andrew V.
Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.
Degree: Biomolecular Engineering and Bioinformatics, 2013, University of California – Santa Cruz
URL: http://www.escholarship.org/uc/item/5284w609
► High-throughput RNA sequencing (RNA-Seq), although still novel, has primarily been applied as a method for assessing differential RNA abundance or mapping of primary structure of…
(more)
▼ High-throughput RNA sequencing (RNA-Seq), although still novel, has primarily been applied as a method for assessing differential RNA abundance or mapping of primary structure of linear transcripts, e.g. inference of splice junctions. I report on two novel applications of RNA-Seq for which I developed computational pipelines. The first (FragSeq) is a coupling of classic enzymatic RNA structure probing with RNA-Seq in order to obtain high-throughput, single-base-resolution endonuclease accessibility maps of entire transcriptomes, thus yielding RNA structure information. A proof-of-principle application of this method on two mouse nuclear RNA samples showed that ssRNA regions of known nuclear ncRNA structures are accurately mapped. Also, mapping of novel structures was validated by follow-up probing. The second application is my pipeline for discovery of RNA circularization from RNA-Seq reads that I applied to a broad unpublished dataset spanning 21 archaeal species and a bacterium, uncovering evidence that C/D RNA guide transcripts are circularized in hyperthermophiles. My findings agree with published findings of circular C/D RNA in three species (P. furiosus, S. acidocaldarius, and S. solfataricus) and provide high-confidence evidence for broad C/D RNA circularization in at least two new species (I. hospitalis and T. kodakaraensis), arguing that this circularization is phylogenetically widespread. Interestingly, the crenarchaeal hyperthermophile P. aerophilum has circularization of transcripts anti-sense to C/D RNAs. This is currently the broadest study of circularization in any domain of life.
Subjects/Keywords: Bioinformatics; archaea; circular RNA; FragSeq; ncRNA; RNA-Seq; RNA structure
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Export
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APA (6th Edition):
Uzilov, A. V. (2013). Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. (Thesis). University of California – Santa Cruz. Retrieved from http://www.escholarship.org/uc/item/5284w609
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Uzilov, Andrew V. “Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.” 2013. Thesis, University of California – Santa Cruz. Accessed January 22, 2021.
http://www.escholarship.org/uc/item/5284w609.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Uzilov, Andrew V. “Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs.” 2013. Web. 22 Jan 2021.
Vancouver:
Uzilov AV. Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. [Internet] [Thesis]. University of California – Santa Cruz; 2013. [cited 2021 Jan 22].
Available from: http://www.escholarship.org/uc/item/5284w609.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Uzilov AV. Novel applications of high-throughput RNA sequencing: mapping RNA structure and discovering circular RNAs. [Thesis]. University of California – Santa Cruz; 2013. Available from: http://www.escholarship.org/uc/item/5284w609
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Louisiana State University
20.
Korde, Asawari.
Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.
Degree: PhD, 2014, Louisiana State University
URL: etd-05232014-193901
;
https://digitalcommons.lsu.edu/gradschool_dissertations/274
► Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically…
(more)
▼ Transcription by RNA polymerase III (Pol III) requires sequential assembly of Pol III-specific transcription factors. At the tRNA gene, the TFIIIC complex recognizes and specifically binds at intragenic promoter elements A-box and B-box and aids the assembly of TFIIIB to upstream of the transcriptional start site. Upon binding, Pol III is recruited near start sites and transcription of tRNA genes is initiated. Apart from transcription of a gene, these bound Pol III complexes influence transcription, chromatin state and genome organization of neighboring RNA polymerase II (Pol II)-transcribed genes. Such effects are known as extra-transcriptional effects of Pol III complex. Our study provides evidence of a unique “extra-transcriptional” activity of assembled Pol III transcription complexes at the tRNA gene that blocks progression of intergenic RNA polymerase II transcription. We demonstrated that the Pol III transcription complex bound to the tRNA gene upstream of the Saccharomyces cerevisiae ATG31 gene protects the ATG31 promoter against readthrough transcriptional interference from the upstream non-coding intergenic SUT467. The protection is predominately mediated by binding of the TFIIIB complex. Failure to block this readthrough resulted in compromised ATG31 translation. Given the recent discovery of widespread pervasive transcription in yeast, protection of neighboring genes from intergenic transcriptional interference may be a key extra-transcriptional function of assembled RNA polymerase III complexes. Our data from RNA-seq analysis demonstrated genome-wide effects of DNA bound Pol III complexes on neighboring chromosomal loci, by comparing expression profiles from tfc6 under-expressing mutants and wild-type S. cerevisiae strains. Reduced TFIIIC occupancy in mutant strains altered Pol II derived transcripts and displayed 5’ or 3’ extension of protein-coding genes, readthrough from non-coding transcripts and increase in the transcription of genes near the potential TFIIIC binding sites, including tRNA genes and putative ETC sites. Interestingly, not all genes in the vicinity of TFIIIC binding sites were transcriptionally mis-regulated, suggesting variable strength of influence on Pol II transcripts by TFIIIC bound sites. Finally, as observed in SUT467-ATG31 readthrough, we anticipated translation defects in 5’ or 3’ extended transcripts in mutants. Overall these genome-wide results suggest much complex regulatory role of Pol III transcription factors bound sites than previously anticipated.
Subjects/Keywords: RNA-seq; tRNA gene; barriers; non-coding RNA; insulators; RNA polymerases
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APA (6th Edition):
Korde, A. (2014). Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274
Chicago Manual of Style (16th Edition):
Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Doctoral Dissertation, Louisiana State University. Accessed January 22, 2021.
etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.
MLA Handbook (7th Edition):
Korde, Asawari. “Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes.” 2014. Web. 22 Jan 2021.
Vancouver:
Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Internet] [Doctoral dissertation]. Louisiana State University; 2014. [cited 2021 Jan 22].
Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274.
Council of Science Editors:
Korde A. Extra-Transcriptional Effects of Chromatin Bound RNA Polymerase III Transcription Complexes. [Doctoral Dissertation]. Louisiana State University; 2014. Available from: etd-05232014-193901 ; https://digitalcommons.lsu.edu/gradschool_dissertations/274
University of Texas – Austin
21.
Qin, Yidan.
Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.
Degree: PhD, Microbiology, 2016, University of Texas – Austin
URL: http://hdl.handle.net/2152/41602
► Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and RNA-seq. TGIRTs…
(more)
▼ Thermostable group II intron reverse transcriptases (TGIRTs) from thermophilic bacteria are advantageous for biotechnological applications that require cDNA synthesis, such as RT-qPCR and
RNA-
seq. TGIRTs have higher thermostability, processivity and fidelity than conventional retroviral RTs, along with a novel end-to-end template-switching activity that attaches
RNA-
seq adapters to target RNAs without
RNA ligation. First, I optimized the TGIRT template-switching method for
RNA-
seq analysis of small non-coding RNAs (ncRNAs). I showed that TGIRT-
seq gives full-length reads of tRNAs, which are refractory to retroviral RTs, and enables identification of a variety of base modifications in tRNAs by distinctive patterns of misincorporated nucleotides. With collaborators, I developed an efficient and quantitative high-throughput tRNA sequencing method, identified RNAs bound by the human interferon-induced protein IFIT5, yielding new insights into its functions in tRNA quality control and innate immunity, and uncovered a novel mRNA-independent mechanism for elongation of nascent peptides. Second, I developed a new, streamlined TGIRT-
seq method for comprehensive analysis of all
RNA size classes in a single
RNA-
seq. This method enables
RNA-
seq library construction from <1 ng of fragmented RNAs in <5 h. By using the method, I showed that human plasma contains large numbers of protein-coding and long ncRNAs together with diverse classes of small ncRNAs, which are mostly present as full-length transcripts. With collaborators, I showed that TGIRT-
seq analysis of circulating RNAs identified potential biomarkers at different stages of multiple myeloma and may provide a sensitive, non-invasive diagnostic tool for a variety of human diseases. Finally, I adapted TGIRTs for use in mapping of
RNA structures and
RNA-protein interaction sites, and identification of
RNA targets of cellular
RNA-binding proteins. My research led to a series of new biological insights, which would have been difficult or impossible to obtain by current methods, and established TGIRTs as a tool for a broad range of applications in
RNA research and diagnostics.
Advisors/Committee Members: Lambowitz, Alan (advisor), Iyer, Vishwanath R (committee member), Krug, Robert M (committee member), Russell, Rick (committee member), Stevens, Scott W (committee member), Sullivan, Christopher S (committee member).
Subjects/Keywords: RNA-seq; Diagnostics; Precision medicine; Non-coding RNA; Circulating RNA
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Manager
APA (6th Edition):
Qin, Y. (2016). Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. (Doctoral Dissertation). University of Texas – Austin. Retrieved from http://hdl.handle.net/2152/41602
Chicago Manual of Style (16th Edition):
Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Doctoral Dissertation, University of Texas – Austin. Accessed January 22, 2021.
http://hdl.handle.net/2152/41602.
MLA Handbook (7th Edition):
Qin, Yidan. “Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine.” 2016. Web. 22 Jan 2021.
Vancouver:
Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Internet] [Doctoral dissertation]. University of Texas – Austin; 2016. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/2152/41602.
Council of Science Editors:
Qin Y. Thermostable group II intron reverse transcriptases and their applications in next generation RNA sequencing, diagnostics, and precision medicine. [Doctoral Dissertation]. University of Texas – Austin; 2016. Available from: http://hdl.handle.net/2152/41602
University of California – Irvine
22.
Le, Rebekah Charney.
The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.
Degree: Biological Sciences, 2016, University of California – Irvine
URL: http://www.escholarship.org/uc/item/22r462c6
► Germ layer specification is one of the earliest developmental events in metazoan organisms, and relies upon the combinatorial interactions of signaling pathways and transcription factors…
(more)
▼ Germ layer specification is one of the earliest developmental events in metazoan organisms, and relies upon the combinatorial interactions of signaling pathways and transcription factors (TFs), and the epigenetic landscape. A complete understanding of the gene regulatory program that contribute to the specification of the mesoderm and endoderm (‘mesendoderm’) in vivo is a crucial unanswered question. The Nodal signaling pathway, which is zygotically activated in the vegetal hemisphere of the early Xenopus embryo, is transcriptionally mediated by the TF Foxh1 and plays a key role in mesendoderm development. It has been suggested that Foxh1 plays dual regulatory roles in transcriptional mediation, and also functions independently of Nodal signaling. However, little is known about the contribution of Foxh1 to the activation of the mesendoderm program via TF binding to cis-regulatory modules (CRMs).Here, I have investigated the early functions of Xenopus Foxh1. I have utilized chromatin immunoprecipitation (ChIP) coupled with deep sequencing to investigate the genome-wide in vivo binding patterns of Foxh1 over the time course of early mesendoderm development, and compared Foxh1 occupancy to the recruitment of RNA polymerase II, epigenetic marks, and zygotic factors. I have found that Foxh1 binding is dynamic and bookmarks the early embryonic genome before zygotic genome activation. Furthermore, this early binding recruits the co-repressor Groucho/Tle. I identified a population of Foxh1 persistent peaks that are occupied throughout early mesendoderm development. These persistent peaks are marked as active enhancers, and recruit Smad2/3 and the zygotic pioneer factor Foxa. Therefore, they are likely critical mesendoderm CRMs, likely pioneered by Foxh1.Further, through mRNA-seq coupled with loss-of-function, I’ve expanded the list of bona-fide direct Foxh1 and Nodal signaling targets throughout mesendoderm development. Foxh1 direct targets appear dynamically regulated across the time course, and I confirm that Foxh1 functions dually as an activator and repressor. Temporal analysis of the expression of Foxh1 repressed targets suggests that Foxh1 plays a role in the regulation of maternal genes.My findings indicate a complex role for maternal Foxh1 at the top of a temporal hierarchy in the regulation of the early mesendoderm gene regulatory program. I propose a model whereby Foxh1 interacts with transcriptional co-repressors and activators in a context-specific fashion to regulate enhancer activation through both time and space. As the roles of Nodal signaling and Foxh1 in mesoderm and endoderm development are conserved among vertebrates, the findings presented here will have broad impacts in the fields of developmental, evolutionary, and stem cell biology.
Subjects/Keywords: Developmental biology; ChIP-seq; endoderm; Foxh1; Groucho/Tle; RNA-seq; Xenopus
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Chicago ·
MLA ·
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CSE |
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to Zotero / EndNote / Reference
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APA (6th Edition):
Le, R. C. (2016). The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. (Thesis). University of California – Irvine. Retrieved from http://www.escholarship.org/uc/item/22r462c6
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Le, Rebekah Charney. “The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.” 2016. Thesis, University of California – Irvine. Accessed January 22, 2021.
http://www.escholarship.org/uc/item/22r462c6.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Le, Rebekah Charney. “The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network.” 2016. Web. 22 Jan 2021.
Vancouver:
Le RC. The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. [Internet] [Thesis]. University of California – Irvine; 2016. [cited 2021 Jan 22].
Available from: http://www.escholarship.org/uc/item/22r462c6.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Le RC. The role of maternal Foxh1 in the activation of the mesendoderm gene regulatory network. [Thesis]. University of California – Irvine; 2016. Available from: http://www.escholarship.org/uc/item/22r462c6
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of California – Berkeley
23.
Roberts, Adam.
Ambiguous fragment assignment for high-throughput sequencing experiments.
Degree: Computer Science, 2013, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/7zx1s4hr
► As the cost of short-read, high-throughput DNA sequencing continues to fall rapidly, new uses for the technology have been developed aside from its original purpose…
(more)
▼ As the cost of short-read, high-throughput DNA sequencing continues to fall rapidly, new uses for the technology have been developed aside from its original purpose in determining the genome of various species. Many of these new experiments use the sequencer as a digital counter for measuring biological activities such as gene expression (RNA-Seq) or protein binding (ChIP-Seq).A common problem faced in the analysis of these data is that of sequenced fragments that are "ambiguous", meaning they resemble multiple loci in a reference genome or other sequence. In early analyses, such ambiguous fragments were ignored or were assigned to loci using simple heuristics. However, statistical approaches using maximum likelihood estimation have been shown to greatly improve the accuracy of downstream analyses and have become widely adopted Optimization based on the expectation-maximization (EM) algorithm are often employed by these methods to find the optimal sets of alignments, with frequent enhancements to the model. Nevertheless, these improvements increase complexity, which, along with an exponential growth in the size of sequencing datasets, has led to new computational challenges.Herein, we present our model for ambiguous fragment assignment for RNA-Seq, which includes the most comprehensive set of parameters of any model introduced to date, as well as various methods we have explored for scaling our optimization procedure. These methods include the use of an online EM algorithm and a distributed EM solution implemented on the Spark cluster computing system. Our advances have resulted in the first efficient solution to the problem of fragment assignment in sequencing.Furthermore, we are the first to create a fully generalized model for ambiguous fragment assignment and present details on how our method can provide solutions for additional high-throughput sequencing assays including ChIP-Seq, Allele-Specific Expression (ASE), and the detection of RNA-DNA Differences (RDDs) in RNA-Seq.
Subjects/Keywords: Computer science; Bioinformatics; chip-seq; expectation-maximization; rna-seq; sequencing
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CSE |
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Manager
APA (6th Edition):
Roberts, A. (2013). Ambiguous fragment assignment for high-throughput sequencing experiments. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/7zx1s4hr
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Roberts, Adam. “Ambiguous fragment assignment for high-throughput sequencing experiments.” 2013. Thesis, University of California – Berkeley. Accessed January 22, 2021.
http://www.escholarship.org/uc/item/7zx1s4hr.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Roberts, Adam. “Ambiguous fragment assignment for high-throughput sequencing experiments.” 2013. Web. 22 Jan 2021.
Vancouver:
Roberts A. Ambiguous fragment assignment for high-throughput sequencing experiments. [Internet] [Thesis]. University of California – Berkeley; 2013. [cited 2021 Jan 22].
Available from: http://www.escholarship.org/uc/item/7zx1s4hr.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Roberts A. Ambiguous fragment assignment for high-throughput sequencing experiments. [Thesis]. University of California – Berkeley; 2013. Available from: http://www.escholarship.org/uc/item/7zx1s4hr
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
University of Southern California
24.
Dai, Chao.
Integrating high-throughput sequencing data to study gene
regulation.
Degree: PhD, Computational Biology and Bioinformatics, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3539
► High-throughput sequencing is a powerful technique for gene regulation study, which can provide information about isoform expression as well as transcription factors / epigenetic factors…
(more)
▼ High-throughput sequencing is a powerful technique for
gene regulation study, which can provide information about isoform
expression as well as transcription factors / epigenetic factors
binding signal measurements. Chromosome conformation capture
followed by high-throughput sequencing were recently applied to
study spatial genome organization and shed light on functional
associations between genome organization and gene regulation. By
integrating genome wide high-throughput sequencing data, this
dissertation investigates gene regulation in three different
layers: co-splicing; coupling between transcription and splicing;
and functional implications of spatial genome organization. ❧ In
the exon co-splicing project, we designed a tensor-based approach
to identify co-spliced exon clusters that frequently appear in
multiple
RNA-
seq datasets. We found that co-splicing clusters can
reveal novel functional groups which cannot be identified by
co-expression clusters, and they can grant new insights of
functions associated with post-transcriptional regulation. Our
results also demonstrated that the same exons can dynamically
participate in different pathways depending on different conditions
and different other exons that are co-spliced. ❧ In the
transcription and splicing coupling project, by using tensor-based
approach to identify frequent coupled clusters on two layered
co-expression networks and co-splicing networks, we demonstrated
that protein-protein interactions between transcription factors and
splicing factors could potentially serve as important mediators for
transcription-splicing coupling. ❧ In spatial genome organization
and genome function association project, we applied our
tensor-based integrative network pattern mining method on a
population of genome structures modeled from chromosome
conformation capture data, and integrated public epigenetic marks
and transcription factors ChIP-
seq and
RNA-
seq data, to
systematically investigate functional implications of spatial
genome organization. Our results strongly demonstrated that
transcriptional regulation and epigenetic regulation are
functionally coupled with spatial genome organization, and
centromeric influence plays an important role to shape spatial
genome organization.
Advisors/Committee Members: Zhou, Xianghong Jasmine (Committee Chair), Waterman, Michael S. (Committee Member), Alber, Frank (Committee Member), Liu, Yan (Committee Member).
Subjects/Keywords: gene regulation; RNA-seq; ChIP-seq; spatial genome organization
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Dai, C. (2015). Integrating high-throughput sequencing data to study gene
regulation. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3539
Chicago Manual of Style (16th Edition):
Dai, Chao. “Integrating high-throughput sequencing data to study gene
regulation.” 2015. Doctoral Dissertation, University of Southern California. Accessed January 22, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3539.
MLA Handbook (7th Edition):
Dai, Chao. “Integrating high-throughput sequencing data to study gene
regulation.” 2015. Web. 22 Jan 2021.
Vancouver:
Dai C. Integrating high-throughput sequencing data to study gene
regulation. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2021 Jan 22].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3539.
Council of Science Editors:
Dai C. Integrating high-throughput sequencing data to study gene
regulation. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/340117/rec/3539
University of Otago
25.
Baker, Estelle Swainson.
Characterisation of the NS1-2 and NS4 proteins of murine norovirus
.
Degree: 2012, University of Otago
URL: http://hdl.handle.net/10523/2320
► Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. Noroviruses belong to the family Caliciviridae and have…
(more)
▼ Human noroviruses are highly infectious viruses that cause the majority of acute, non-bacterial epidemic gastroenteritis cases worldwide. Noroviruses belong to the family Caliciviridae and have a positive-sense
RNA genome of around 7.5 kb. Murine norovirus is a useful model for the uncultivable human strains, and has a 7.4 kb genome with four open reading frames (ORFs). Two of these, ORF2 and ORF3, encode structural proteins and ORF4 encodes a virulence factor. The first open reading frame (ORF1) encodes a polyprotein that is cleaved by the viral protease into six nonstructural proteins. There is limited functional and biophysical information available for two of these nonstructural proteins, NS1-2 and NS4. The aims of this research were to characterise these two proteins.
The NS1-2 protein lacks any significant sequence similarity to other viral or cellular proteins. Bioinformatic analyses identified an inherently disordered region (residues 1 – 142) in the highly divergent N-terminal region of the NS1-2 protein. Expression and purification of the NS1-2 protein of murine norovirus confirmed these predictions by identifying features typical of an inherently disordered protein. These were a biased amino acid composition with enrichment in the disorder promoting residues serine and proline, a lack of predicted secondary structure, a hydrophilic nature, an aberrant electrophoretic migration, an increased Stokes radius similar to that predicted for a protein from the pre-molten globule family, a high sensitivity to thermolysin proteolysis and a circular dichroism spectrum typical of an inherently disordered protein. The purification of the NS1-2 protein identified the presence of an NS1-2 dimer when expressed in Escherichia coli, which was also identified in transfected HEK293T cells and MNV-infected RAW264.7 cells.
The NS4 protein is often referred to as the 3A-like protein due to a similar position in the genome as the 3A protein of poliovirus. However, NS4 shares only limited sequence similarity to polio 3A. The NS4 protein of murine norovirus was expressed in Escherichia coli and purified for the generation of a polyclonal antibody.
Whole transcriptome
RNA-
Seq analysis was conducted on transfected RAW264.7 cells to provide important leads on functional roles, effects and host cell responses to in vitro transcripts encoding the complete MNV genome, the ORF1 nonstructural polyprotein, the full-length NS1-2 protein and the disordered region of NS1-2. Each transfected cell sample showed an upregulation in anti-apoptotic genes and a downregulation of pro-apoptotic genes, suggesting that MNV, and in particular the disordered region of NS1-2, manipulates the induction of apoptosis. A downregulation of sterol lipid synthesis genes and an upregulation of Th1-type chemokines were observed in MNV- and ORF1-transfected cells. NS1-2-transfected cells showed an increased expression for genes encoding intercellular junctions and regulatory proteins, indicating that NS1-2 is likely to have a multi-functional role affecting…
Advisors/Committee Members: Ward, Vernon (advisor).
Subjects/Keywords: Norovirus;
RNA-Seq;
Disorder;
NS1-2;
NS4
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Baker, E. S. (2012). Characterisation of the NS1-2 and NS4 proteins of murine norovirus
. (Doctoral Dissertation). University of Otago. Retrieved from http://hdl.handle.net/10523/2320
Chicago Manual of Style (16th Edition):
Baker, Estelle Swainson. “Characterisation of the NS1-2 and NS4 proteins of murine norovirus
.” 2012. Doctoral Dissertation, University of Otago. Accessed January 22, 2021.
http://hdl.handle.net/10523/2320.
MLA Handbook (7th Edition):
Baker, Estelle Swainson. “Characterisation of the NS1-2 and NS4 proteins of murine norovirus
.” 2012. Web. 22 Jan 2021.
Vancouver:
Baker ES. Characterisation of the NS1-2 and NS4 proteins of murine norovirus
. [Internet] [Doctoral dissertation]. University of Otago; 2012. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/10523/2320.
Council of Science Editors:
Baker ES. Characterisation of the NS1-2 and NS4 proteins of murine norovirus
. [Doctoral Dissertation]. University of Otago; 2012. Available from: http://hdl.handle.net/10523/2320
University of California – Berkeley
26.
Combs, Peter Acuña.
Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes.
Degree: Biophysics, 2015, University of California – Berkeley
URL: http://www.escholarship.org/uc/item/81h3q2xh
► A complex, spatially and temporally dynamic network of gene expression underlies proper metazoan development, yet methods have not previously existed to assay this network in…
(more)
▼ A complex, spatially and temporally dynamic network of gene expression underlies proper metazoan development, yet methods have not previously existed to assay this network in an efficient, systematic manner. Brute-force application of in situ imaging has been used to painstakingly assay the network, but is impractical to apply to assay the complete gene expression network in multiple mutant conditions. Sequencing, in contrast, is fast and genome-wide, but is generally applied to homogenized tissues, discarding any spatial information.In the first phase of my research, I have developed methods for performing mRNAseq to globally profile gene expression in dissected subsets of single Drosophila embryos. The patterns I measure are consistent between replicates, and also faithfully reproduce patterns already known from in situ hybridization experiments. However, the global nature of this experiment also reveals spatial patterning in many genes that have not been successfully assayed, even in relatively large-scale projects. Furthermore, I demonstrate that this can be used across samples from different developmental time points to produce a genome-wide developmental atlas of zygotic gene activation.Because the small sample size of slices of single embryos limited the ability to use standard cDNA library preparation protocols, I next assayed a number of previously published protocols that were specifically designed for minute samples. Previous literature had not addressed whether these protocols would be suitable for reconstructing spatial patterns, and I was particularly concerned that pre-amplification steps would introduce unacceptable non-linearities in the data. Upon analyzing the results, however, I determined that all the protocols I tried were acceptable, and all approximately equally good. I also investigated a few modifications to one of the protocols that reduces the cost of library preparation such that it is no longer the primary limiting factor in terms of number of samples to be sequenced.Finally, with these methods well refined, I have sliced and sequenced embryos with severe genetic perturbations to maternally provided factors at the head of the patterning network. Comparing embryos deficient in the key pioneer factor zelda, I have revealed that this lethal mutant is nevertheless able to correctly produce the majority of gene expression patterns in the wild-type embryo. Embryos lacking the maternally provided activator bicoid show a greater loss of proper patterning, including the surprising result of ubiquitous over-expression of a number of genes. Simple models of local action of bicoid cannot easily account for this change. Surveying bicoid over-expression mutants and hunchback knock-downs has also yielded a large number of unexpected patterning changes. All of these changes recapitulate previously measured patterning changes, but also highlight new avenues to investigate.
Subjects/Keywords: Biology; Genetics; Bioinformatics; cryosliced; Drosophila; RNA-seq
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APA ·
Chicago ·
MLA ·
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CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Combs, P. A. (2015). Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes. (Thesis). University of California – Berkeley. Retrieved from http://www.escholarship.org/uc/item/81h3q2xh
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Combs, Peter Acuña. “Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes.” 2015. Thesis, University of California – Berkeley. Accessed January 22, 2021.
http://www.escholarship.org/uc/item/81h3q2xh.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Combs, Peter Acuña. “Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes.” 2015. Web. 22 Jan 2021.
Vancouver:
Combs PA. Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes. [Internet] [Thesis]. University of California – Berkeley; 2015. [cited 2021 Jan 22].
Available from: http://www.escholarship.org/uc/item/81h3q2xh.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Combs PA. Sequencing mRNA from cryosliced Drosophila embryos to screen genome-wide patterning changes. [Thesis]. University of California – Berkeley; 2015. Available from: http://www.escholarship.org/uc/item/81h3q2xh
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Oregon State University
27.
Zhuo, Bin.
Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.
Degree: PhD, Statistics, 2016, Oregon State University
URL: http://hdl.handle.net/1957/59543
► Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the…
(more)
▼ Differential expression (DE) analysis is a key task in gene expression study, because it uncovers the association between expression levels of a gene and the covariates of interest. This dissertation pertains to two particular aspects of DE analysis—identifying stably expressed genes for count normalization and accounting for correlation between DE test statistics in gene-set test.
RNA-Sequencing (
RNA-
Seq) has become the tool of choice for measuring gene expression over the past few years, and data generated from
RNA-
Seq experiments are the focus of this thesis.
Identifying stably expressed genes is useful for count normalization and DE analysis. We examined
RNA-
Seq data on 211 biological samples from 24 different experiments conducted by different labs, and identified genes that are stably expressed across samples, treatment conditions, and experiments. We fit a Poisson log-linear mixed-effect model to the count data, and decomposed the total variance into between-sample, between-treatment and between-experiment variance components. The variance component analysis that we explore here is a first step towards understanding the sources and nature of the
RNA-
Seq count variation. The stability ranking of genes, when quantified by a numerical stability measure, is dependent on several factors: the background sample set and the reference gene set used for count normalization, the technology used to measure gene expression, and the specific stability measure. Since DE is measured by relative frequencies, we argue that DE is a relative concept. We advocate using an explicit reference gene set for count normalization to improve interpretability of DE results, and recommend using a common reference gene set when analyzing multiple
RNA-
Seq experiments to avoid potential inconsistent conclusions.
We investigate the relationship between correlation among test statistics and the correlation of underlying observed data. For false discovery control (FDR) procedures and gene-set tests, pooling DE test statistics together is a frequently used idea and the correlation among test statistics needs to be taken into account. The sample correlation of observed data is often used to approximate the test statistics correlation. We show, however, that such an approximation is only valid under limited settings. In particular, we derive a formula for correlation between test statistics when they take a specific form, and as a special case, we present the exact expression of test-statistic correlation for equal-variance two-sample t-test statistic under bivariate normal assumption. We conclude that test-statistic correlation is weaker than the correlation of underlying observed data (normally distributed) in the context of equal-variance two-sample t-test.
Competitive gene-set test is a widely used tool for interpreting high-throughput biological data, such as gene expression and proteomics data. It aims at testing categories of genes for enriched association signals in a list of genes inferred from genome-wide data. Most conventional…
Advisors/Committee Members: Di, Yanming (advisor), Emerson, Sarah (committee member).
Subjects/Keywords: RNA-Seq; Gene expression – Statistical methods
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Zhuo, B. (2016). Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/59543
Chicago Manual of Style (16th Edition):
Zhuo, Bin. “Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.” 2016. Doctoral Dissertation, Oregon State University. Accessed January 22, 2021.
http://hdl.handle.net/1957/59543.
MLA Handbook (7th Edition):
Zhuo, Bin. “Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes.” 2016. Web. 22 Jan 2021.
Vancouver:
Zhuo B. Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. [Internet] [Doctoral dissertation]. Oregon State University; 2016. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/1957/59543.
Council of Science Editors:
Zhuo B. Higher-level Analysis of RNA-Seq Experiment: Multiple Data Sets and Multiple Genes. [Doctoral Dissertation]. Oregon State University; 2016. Available from: http://hdl.handle.net/1957/59543
Texas A&M University
28.
Carrow, James Kenning.
Engineering Stem Cell Responses with Two-Dimensional Nanomaterials.
Degree: PhD, Biomedical Engineering, 2018, Texas A&M University
URL: http://hdl.handle.net/1969.1/173992
► Two-dimensional (2D) nanomaterials are an emerging class of biomaterials that have garnered unprecedented attention due to their unique atomically thin, layered, and well-defined structure. These…
(more)
▼ Two-dimensional (2D) nanomaterials are an emerging class of biomaterials that have garnered unprecedented attention due to their unique atomically thin, layered, and well-defined structure. These nanomaterials, however, have limited investigations into their cytocompatibility and potential use in regenerative medicine particularly from the perspective of 3D scaffolds. Here we report two chemically unique 2D nanomaterials and their biophysical and biochemical interactions with stem cells. The first is a naturally occurring nanosilicate which is made up of a unique combination of minerals (Na
+, L
i+, Mg
2+, Si(OH)v4) within an octahedral sheet sandwiched between two tetrahedral lattices (Laponite XLG®). The second is a transition metal dichalcogenide (TMD) of molybdenum disulfide (MoSv2) which forms 2D sheets nanometers in thickness. Using molecular biology techniques that capture a holistic snapshot of cell signaling, like
RNA-sequencing (
RNA-
seq), we can begin to examine mechanisms behind changes in behavior. With this information, we can then interrogate specific pathways of interest to generate a desired cell response. Furthermore, we can incorporate these nanomaterials into polymeric scaffolds to localize both cells and bioactive materials for delivery in vivo. Specifically, we utilized formulations of the polysaccharide kappa-Carrageenan with the nanosilicates and a thiol-modified 4-arm polyethylene glycol (PEG) with 2D MoSv2. Using these studies as a framework, researchers can begin to tailor new polymeric scaffolds around emergent 2D nanomaterials for a variety of regenerative applications including bioprinting.
Advisors/Committee Members: Gaharwar, Akhilesh K (advisor), Kaunas, Roland (committee member), Grunlan, Melissa (committee member), Watts, Ashlee (committee member).
Subjects/Keywords: RNA-seq; Nanomaterials; Stem cells; Regenerative Engineering
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Carrow, J. K. (2018). Engineering Stem Cell Responses with Two-Dimensional Nanomaterials. (Doctoral Dissertation). Texas A&M University. Retrieved from http://hdl.handle.net/1969.1/173992
Chicago Manual of Style (16th Edition):
Carrow, James Kenning. “Engineering Stem Cell Responses with Two-Dimensional Nanomaterials.” 2018. Doctoral Dissertation, Texas A&M University. Accessed January 22, 2021.
http://hdl.handle.net/1969.1/173992.
MLA Handbook (7th Edition):
Carrow, James Kenning. “Engineering Stem Cell Responses with Two-Dimensional Nanomaterials.” 2018. Web. 22 Jan 2021.
Vancouver:
Carrow JK. Engineering Stem Cell Responses with Two-Dimensional Nanomaterials. [Internet] [Doctoral dissertation]. Texas A&M University; 2018. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/1969.1/173992.
Council of Science Editors:
Carrow JK. Engineering Stem Cell Responses with Two-Dimensional Nanomaterials. [Doctoral Dissertation]. Texas A&M University; 2018. Available from: http://hdl.handle.net/1969.1/173992
Penn State University
29.
Imperio, Caesar Gerald.
From behavior to epigenetics: Individual differences in heroin addiction.
Degree: 2015, Penn State University
URL: https://submit-etda.libraries.psu.edu/catalog/26303
► Heroin addiction is a disease of chronic relapse that harms the individual through the devaluation of natural rewards in favor of finding and using drugs.…
(more)
▼ Heroin addiction is a disease of chronic relapse that harms the individual through the devaluation of natural rewards in favor of finding and using drugs. Although destructive, studies have shown that approximately 50% of the human population will transition from controlled heroin use to addiction. Given the variability, there is a need to determine why certain individuals respond differently to heroin. Therefore the goal of this dissertation is to determine at the behavioral and molecular levels why individual differences in addiction-like behavior occur with heroin. In Chapter 2, I developed an animal model that used avoidance of a heroin-paired saccharin cue to stratify rats on their addiction-like behaviors. Greater avoidance of the reward cue was linked with greater drug taking, drug loading, drug escalation, and increased relapse-like behaviors. Using next generation sequencing in Chapter 3, avoidance of the drug-paired taste cue was linked to individual differences in gene expression in the nucleus accumbens. In Chapter 4, I used taste reactivity to assess the perceived hedonic value of the natural reward cue as it came to predict the opportunity to self-administer heroin. Previous cocaine studies have shown that intraoral administration of a drug-paired taste cue elicits negative taste reactivity (gaping) and greater gaping is correlated with greater drug taking behaviors. The results show that, unlike cocaine, intraoral delivery of a heroin-paired taste cue does not support either robust or sustained aversive taste reactivity behavior. Lastly, given the profound effect the environment has on the development of addiction, environmental enrichment was employed to determine if persistent enrichment status can attenuate the development of addiction-like behavior (Chapter 5). Enrichment was shown to attenuate the motivation to work for heroin and prevent drug-seeking behaviors following a period of drug abstinence. Enrichment also buffered the effects of heroin exposure on mRNA expression in the brain. Furthermore, changes in neural DNA methylation were found due to heroin exposure and enrichment status. Taken together, the data presented in this thesis demonstrate the dynamic interplay between an individual’s genetic background and the environment on the development and expression of opiate addiction and associated epigenetic mediators.
Advisors/Committee Members: Patricia Sue Grigson Kennedy, Dissertation Advisor/Co-Advisor, Scott C Bunce, Committee Member, Willard M Freeman, Special Member, Robert G Levenson, Committee Member, Victor J Ruiz Velasco, Committee Member.
Subjects/Keywords: Addiction; Heroin; Reward; Epigenetics; Enrichment; RNA-seq
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APA (6th Edition):
Imperio, C. G. (2015). From behavior to epigenetics: Individual differences in heroin addiction. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/26303
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Chicago Manual of Style (16th Edition):
Imperio, Caesar Gerald. “From behavior to epigenetics: Individual differences in heroin addiction.” 2015. Thesis, Penn State University. Accessed January 22, 2021.
https://submit-etda.libraries.psu.edu/catalog/26303.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
MLA Handbook (7th Edition):
Imperio, Caesar Gerald. “From behavior to epigenetics: Individual differences in heroin addiction.” 2015. Web. 22 Jan 2021.
Vancouver:
Imperio CG. From behavior to epigenetics: Individual differences in heroin addiction. [Internet] [Thesis]. Penn State University; 2015. [cited 2021 Jan 22].
Available from: https://submit-etda.libraries.psu.edu/catalog/26303.
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Council of Science Editors:
Imperio CG. From behavior to epigenetics: Individual differences in heroin addiction. [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/26303
Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation
Texas Tech University
30.
Kunder, Komal Ramesh.
Molecular landscape of cotton fibers in early elongation.
Degree: MS, Biotechnology, 2013, Texas Tech University
URL: http://hdl.handle.net/2346/73858
► Cotton fibers are the dominant source of natural fibers used in the textile industry and contribute significantly to the world economy. Adverse environmental conditions negatively…
(more)
▼ Cotton fibers are the dominant source of natural fibers used in the textile industry and contribute significantly to the world economy. Adverse environmental conditions negatively affect fiber characteristics, especially when the fibers are in the elongation phase of development. Improvement in the yield and quality of cotton fibers requires the identification of the molecular networks involved in fiber development. In this research, we have analyzed cotton fiber transcriptome and proteome in the early elongation phase using
RNA-
Seq and mass spectrometry, to identify the genes and proteins involved in different pathways altered during fiber development. TruSeq
RNA sample preparation kit was used to prepare cDNA libraries from
RNA extracted from Upland cotton cultivar TM-1 cotton fibers samples at 3 and 5 days post-anthesis (DPA). These libraries were sequenced using 151 bp, paired-end Illumina sequencing which produced 6,570,054 and 7,063,378 reads from 3 DPA and 5 DPA libraries, respectively. The de novo assembly of these raw reads with NGen identified 20,270 contigs in 3 DPA and 20,339 contigs in 5 DPA. The raw reads were mapped on the reference early fiber transcriptome and differential gene expression was estimated by QSeq (DNASTAR genome suite). A total of 3,177 transcripts were recognized as differentially expressed with 95% probability and at least a 2-fold change between 3 DPA and 5 DPA. These transcripts were annotated using Mercator and mapped to biological pathways using MapMan version 3.5.1. The up-regulated transcripts at 5 DPA belonged to cell-wall modification, phospholipid and sphingolipid synthesis, solute and water transporters, cytoskeletal elements and phytohormone categories; processes that were involved in cell wall extension, hinting that the fibers at this stage are involved in loosening the cell wall in anticipation of the rapid fiber elongation beyond 5 DPA. The NGen assembled transcriptomes from 6 stages of fiber development, 3 DPA, 5 DPA, 11 DPA, 17 DPA, 21 DPA and 24 DPA, were re-assembled using CAP3 assembly software to generate the cotton fiber transcriptome. We have also created a reference fiber proteome database from the fiber specific transcriptome containing 374,562 possible protein sequences for protein identification. This is the first report on the generation of a transcriptome and a proteome of the elongating cotton fibers using
RNA-
Seq. These databases form a significant source of information, and will contribute towards research on the improvement of cotton fiber characteristics.
Advisors/Committee Members: Zabet-Moghaddam, Masoud (committee member), Kottapalli, Kameswara R (committee member), Payton, Paxton (committee member), San Francisco, Susan (Committee Chair).
Subjects/Keywords: Cotton Fibers; Transcriptomics; RNA-seq; Mass Spectrometry
Record Details
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Record Details
Similar Records
Cite
« Share
❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kunder, K. R. (2013). Molecular landscape of cotton fibers in early elongation. (Masters Thesis). Texas Tech University. Retrieved from http://hdl.handle.net/2346/73858
Chicago Manual of Style (16th Edition):
Kunder, Komal Ramesh. “Molecular landscape of cotton fibers in early elongation.” 2013. Masters Thesis, Texas Tech University. Accessed January 22, 2021.
http://hdl.handle.net/2346/73858.
MLA Handbook (7th Edition):
Kunder, Komal Ramesh. “Molecular landscape of cotton fibers in early elongation.” 2013. Web. 22 Jan 2021.
Vancouver:
Kunder KR. Molecular landscape of cotton fibers in early elongation. [Internet] [Masters thesis]. Texas Tech University; 2013. [cited 2021 Jan 22].
Available from: http://hdl.handle.net/2346/73858.
Council of Science Editors:
Kunder KR. Molecular landscape of cotton fibers in early elongation. [Masters Thesis]. Texas Tech University; 2013. Available from: http://hdl.handle.net/2346/73858
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Open Access Theses and Dissertations