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Series GSE36212 Query DataSets for GSE36212
Status Public on Aug 30, 2012
Title Promoter activity profiling throughout the Drosophila life cycle reveals role of transposons in regulatory innovation
Organism Drosophila melanogaster
Experiment type Expression profiling by high throughput sequencing
Summary Since their discovery, transposable elements have been proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, in particular by providing transcription start sites (TSSs) for host genes. To investigate their contribution to developmental gene expression, we developed RAMPAGE, a high-throughput 5'-complete cDNA sequencing approach to accurately discover TSSs, characterize their transcripts, and quantify their expression. This strategy, which directly delineates the expression profiles of individual promoters and was designed to offer optimal sample multiplexing capabilities, represents an advantageous alternative to standard RNA-Seq for a wide range of transcriptome profiling applications. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive dataset that represents the first developmental timecourse of promoter usage. We found that over 40% of developmentally expressed genes have at least 2 promoters, and that alternative promoters generally implement distinct regulatory programs. Transposons harbor TSSs driving the expression of hundreds of annotated genes, and they often impart their own expression specificity upon the genes they regulate. Detailed analysis of particular transposons identified sequence elements encoding these regulatory properties. Our results show that transposable elements contribute significantly to the generation of standing variation and to the evolution of gene regulatory networks, by distributing stereotyped regulatory modules throughout the genome.
Overall design This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression throughout 36 stages of the life cycle of Drosophila melanogaster. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. Embryos, larvae, pupae and adult flies were collected at specific stages of development, and RAMPAGE profiles were established for pools of whole organisms. The data was analyzed using custom scripts and algorithms that are all available upon request.

Supplementary files: bigWig coverage by cDNA 5' ends (+ strand). bigWig coverage by cDNA 5' ends (- strand).
Dmel_All_RAMPAGE_peaks.bed: BED file describing all RAMPAGE peaks.
Dmel_GeneTSS_RAMPAGE_peaks.bed: BED file describing all peaks attributed to annotated genes.
GeneTSS_expression_RAMPAGE_RPM.txt: Expression matrix for all genic peaks (RPM: reads per million).
Transposon_expression_RAMPAGE_RPM.txt: Expression matrix for all RepeatMasker-annotated transposon classes (RPM: reads per million).
Genome build: dm3
Contributor(s) Batut P, Dobin A, Plessy C, Carninci P, Gingeras TR
Citation(s) 22936248, 29260710
Submission date Mar 01, 2012
Last update date Aug 01, 2019
Contact name Philippe Batut
Phone 516-422-4122
Organization name CSHL
Lab Gingeras
Street address 500 Sunnyside Blvd.
City Woodbury
State/province NY
ZIP/Postal code 11797
Country USA
Platforms (2)
GPL11203 Illumina Genome Analyzer IIx (Drosophila melanogaster)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (36)
GSM883763 Dmel01_E01h
GSM883764 Dmel02_E02h
GSM883765 Dmel03_E03h
This SubSeries is part of SuperSeries:
GSE36213 Profiling of transcription start site expression in Drosophila and the human K562 cell line using RAMPAGE
SRA SRP011193
BioProject PRJNA155825

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE36212_Dmel_All_RAMPAGE_peaks.bed.gz 386.9 Kb (ftp)(http) BED 4.3 Mb (ftp)(http) BW 4.3 Mb (ftp)(http) BW
GSE36212_Dmel_GeneTSS_RAMPAGE_peaks.bed.gz 322.6 Kb (ftp)(http) BED
GSE36212_GeneTSS_expression_RAMPAGE_RPM.txt.gz 1.9 Mb (ftp)(http) TXT
GSE36212_RAW.tar 33.0 Mb (http)(custom) TAR (of BW)
GSE36212_Transposon_expression_RAMPAGE_RPM.txt.gz 37.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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