The developmental transcriptome of Drosophila melanogaster
Brenton R. Graveley,Angela N. Brooks,Joseph W. Carlson,Michael O. Duff,Jane M. Landolin,Li Yang,Carlo G. Artieri,Marijke J. van Baren,Nathan Boley,Benjamin W. Booth,James B. Brown,Lucy Cherbas,Carrie A. Davis,Alexander Dobin,Renhua Li,Wei Lin,John H. Malone,Nicolas R. Mattiuzzo,David Scott Miller,David Sturgill,Brian B. Tuch,Brian B. Tuch,Chris Zaleski,Dayu Zhang,Marco Blanchette,Marco Blanchette,Sandrine Dudoit,Brian D. Eads,Richard E. Green,Ann S. Hammonds,Lichun Jiang,Phil Kapranov,Laura Langton,Norbert Perrimon,Jeremy E. Sandler,Kenneth H. Wan,Aarron T. Willingham,Yu Zhang,Yi Zou,Justen Andrews,Peter J. Bickel,Steven E. Brenner,Michael R. Brent,Peter Cherbas,Thomas R. Gingeras,Thomas R. Gingeras,Roger A. Hoskins,Thomas C. Kaufman,Brian Oliver,Susan E. Celniker +49 more
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TLDR
111,195 new elements are identified, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches.Abstract:
Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless, its genome still contains unannotated coding and non-coding genes, transcripts, exons and RNA editing sites. Full discovery and annotation are pre-requisites for understanding how the regulation of transcription, splicing and RNA editing directs the development of this complex organism. Here we used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages. We identified 111,195 new elements, including thousands of genes, coding and non-coding transcripts, exons, splicing and editing events, and inferred protein isoforms that previously eluded discovery using established experimental, prediction and conservation-based approaches. These data substantially expand the number of known transcribed elements in the Drosophila genome and provide a high-resolution view of transcriptome dynamics throughout development.read more
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Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
Cole Trapnell,Adam Roberts,Loyal A. Goff,Loyal A. Goff,Loyal A. Goff,Geo Pertea,Daehwan Kim,Daehwan Kim,David R. Kelley,David R. Kelley,Harold Pimentel,Steven L. Salzberg,John L. Rinn,John L. Rinn,Lior Pachter +14 more
TL;DR: This protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results, which takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time.
Journal ArticleDOI
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
Charity W. Law,Charity W. Law,Yunshun Chen,Yunshun Chen,Wei Shi,Wei Shi,Gordon K. Smyth,Gordon K. Smyth +7 more
TL;DR: New normal linear modeling strategies are presented for analyzing read counts from RNA-seq experiments, and the voom method estimates the mean-variance relationship of the log-counts, generates a precision weight for each observation and enters these into the limma empirical Bayes analysis pipeline.
Journal ArticleDOI
Spatial reconstruction of single-cell gene expression data
TL;DR: Seurat is a computational strategy to infer cellular localization by integrating single-cell RNA-seq data with in situ RNA patterns, and correctly localizes rare subpopulations, accurately mapping both spatially restricted and scattered groups.
Journal ArticleDOI
Differential analysis of gene regulation at transcript resolution with RNA-seq
Cole Trapnell,David G. Hendrickson,David G. Hendrickson,Martin Sauvageau,Martin Sauvageau,Loyal A. Goff,Loyal A. Goff,John L. Rinn,John L. Rinn,Lior Pachter +9 more
TL;DR: Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries, robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes.
Journal ArticleDOI
Cell-type specific features of circular RNA expression.
TL;DR: Using an improved computational approach for circular RNA identification, widespread circular RNA expression is found in Drosophila melanogaster and it is estimated that in humans, circular RNA may account for 1% as many molecules as poly(A) RNA.
References
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Cole Trapnell,Cole Trapnell,Brian A. Williams,Geo Pertea,Ali Mortazavi,Gordon Kwan,Marijke J. van Baren,Steven L. Salzberg,Barbara J. Wold,Lior Pachter +9 more
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Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
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TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Journal ArticleDOI
Alternative Isoform Regulation in Human Tissue Transcriptomes
Eric T. Wang,Rickard Sandberg,Rickard Sandberg,Shujun Luo,Irina Khrebtukova,Lu Zhang,Christine Mayr,Stephen F. Kingsmore,Gary P. Schroth,Christopher B. Burge +9 more
TL;DR: An in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments yielding a digital inventory of gene and mRNA isoform expression suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
Journal ArticleDOI
Mutations affecting segment number and polarity in Drosophila
TL;DR: The phenotypes of the mutant embryos indicate that the process of segmentation involves at least three levels of spatial organization: the entire egg as developmental unit, a repeat unit with the length of two segments, and the individual segment.