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Series GSE33905 Query DataSets for GSE33905
Status Public on Nov 23, 2011
Title Identification of polyA sites in Drosophila melanogaster
Project modENCODE
Organism Drosophila melanogaster
Experiment type Other
Summary The 3' ends of most Drosophila melanogaster genes are poorly annotated or are determined by only a single EST or cDNA clone. To enhance the annotation of poly(A) site use in Drosophila, we performed deep sequencing on RNA isolated from 29 dissected tissues using an approach designed to enrich for poly(A) spanning reads. From these experiments, we identified 1.4 million poly(A) spanning reads leading to the identification of many new poly(A) sites and the identification of many tissue-specific poly(A) sites.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
 
Overall design RNA from 29 dissected Drosophila melanogaster tissues (in duplicate) were used to prepare polyA enriched RNA-Seq libraries. Briefly, total RNA was poly(A) selected, fragmented, and ligated to 5' and 3' RNA linkers. These libraries were amplified using Illumina paired-end primers, and subsequently reamplified using a 3' primer complementary to the 3' adapter but containing 6 Ts at the 3' end. The libraries were also multiplexed and up to 12 samples mixed per lane and sequenced on an Illumina GAIIx using paired-end 76 bp reads, or an illumina HiSeq 2000 using paired-end 100 bp reads. All reads were mapped to the Drosophila melanogaster genome to identify unmapped reads. Unmapped reads containing at least 10 A residues at the 3' end were identified, the terminal A residues trimmed, realigned to the genome to identify uniquely mapped reads. Such reads were identified as polyA spanning reads
Web link http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/info/ENCODE.html
 
Contributor(s) Graveley BR, Smibert P, Miura P, Westholm JO, Shenker S, May G, Duff MO, Zhang D, Eads BD, Carlson J, Brown B, Eisman RC, Andrews J, Kaufman T, Cherbas P, Lai EC, Celniker SE
Citation(s) 22685694
BioProject PRJNA63463
Submission date Nov 23, 2011
Last update date May 15, 2019
Contact name Brenton R Graveley
E-mail(s) graveley@uchc.edu
Phone 860-679-2090
Organization name University of Connecticut Health Center
Department Genetics and Genome Sciences
Street address 400 Farmington Avenue
City Farmington
State/province CT
ZIP/Postal code 06030-3301
Country USA
 
Platforms (2)
GPL11203 Illumina Genome Analyzer IIx (Drosophila melanogaster)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (58)
GSM838746 PolyA Spanning Reads from Drosophila melanogaster, RNA ID=553
GSM838747 PolyA Spanning Reads from Drosophila melanogaster, RNA ID=509
GSM838748 PolyA Spanning Reads from Drosophila melanogaster, RNA ID=538
Relations
SRA SRP009459

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
GSE33905_RAW.tar 17.6 Mb (http)(custom) TAR (of GFF)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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