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Sample GSM838778 Query DataSets for GSM838778
Status Public on Nov 23, 2011
Title PolyA Spanning Reads from Drosophila melanogaster, RNA ID=550
Sample type SRA
 
Source name mated female, eclosion + 20 days, heads
Organism Drosophila melanogaster
Characteristics strain: Oregon R
tissue: Head
development stage: Adult, Eclosion + 20 days
gender: Female
mating status: Mated
flow cell: B81CG2ABXX
lane: 2
barcode: GATCAG
Treatment protocol None.
Growth protocol Oregon R Animals were grown under standard laboratory conditions.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from tissues dissected from Oregon R animals in biological duplicates. Strand-specific RNA-seq libraries were prepared using pre-release Directional mRNA-seq Library Kits (Illumina). Briefly, poly(A)+ RNA was isolated by oligo-dT selection, fragmented, and treated with phosphatase and polynucleotide kinase to repair the ends. 3’ and 5’ RNA adapters were then sequentially ligated to the RNA fragments and reverse transcribed using a primer complementary to the 3’ linker. The libraries were then PCR amplified. One nanogram of the strand-specific RNA-Seq libraries were reamplified by PCR using a primer complementary to the 5’ adapter and a second primer complementary to the 3’ adapter with six T residues at the 3’ end. After 10 rounds of amplification, the 3’ primer with the T extension was replaced with a 3’ primer complementary to the adapter with a 5’ extension containing a 6 nt index sequence and a sequence complementary to the flow cell primer. After an additional 15 rounds of amplication, the libraries were quantitated, 10-12 libraries were pooled together and sequenced.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description PolyA Spanning Reads from Drosophila melanogaster, RNA ID=550,Flow cell=B81CG2ABXX,Lane=2,Barcode=GATCAG,Adult, Mated Female, Eclosion + 20 days,Head
Adult, Mated Female, Eclosion + 20 days
Data processing 550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_plus.gff; genome build: dm3
550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_minus.gff; genome build: dm3
Reads were split into the respective samples using the index sequence. Reads were simultaneously aligned to the dm3 genome and splice junctions using Bowtie (Langmead, 2010) and SPA (Graveley et al., 2011). To identify polyA-spanning reads, reads that failed to align to the genome were examined to identify cases where the first read contained >10 A residues at the 3’ end or the second read contained >10 T residues at the 5’ end. The terminal A or T residues were trimmed from the reads and uniquely aligned polyA-spanning reads identified using Bowtie.
 
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
 
Platform ID GPL13304
Series (1)
GSE33905 Identification of polyA sites in Drosophila melanogaster
Relations
Reanalyzed by GSM3275953
SRA SRX109286
BioSample SAMN00760789

Supplementary file Size Download File type/resource
GSM838778_550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_minus.gff.gz 207.6 Kb (ftp)(http) GFF
GSM838778_550_AdMateF_20d_head_B81CG2ABXX_GATCAG_2_pA_plus.gff.gz 712.5 Kb (ftp)(http) GFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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