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| Status |
Public on Nov 23, 2011 |
| Title |
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=587 |
| Sample type |
SRA |
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| Source name |
Pupae, WPP+2d, CNS
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R
tissue: Central Nervous System
development stage: White Pre-Pupae + 2 days
flow cell: B81CG2ABXX
lane: 4
barcode: TGACCA
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| Treatment protocol |
None.
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| Growth protocol |
Oregon R Animals were grown under standard laboratory conditions.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PolyA Spanning Reads from Drosophila melanogaster, RNA ID=587,Flow cell=B81CG2ABXX,Lane=4,Barcode=TGACCA,White Pre-Pupae + 2 days,Central Nervous System
White Pre-Pupae + 2 days
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| Data processing |
587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_pA_plus.gff; genome build: dm3
587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_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.
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| Submission date |
Nov 23, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Brenton R Graveley |
| E-mail(s) |
[email protected]
|
| Phone |
860-679-2090
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| Organization name |
University of Connecticut Health Center
|
| Department |
Genetics and Genome Sciences
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| Street address |
400 Farmington Avenue
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| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-3301 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE33905 |
Identification of polyA sites in Drosophila melanogaster |
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| Relations |
| Reanalyzed by |
GSM3275972 |
| SRA |
SRX109305 |
| BioSample |
SAMN00760808 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM838797_587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_pA_minus.gff.gz |
142.9 Kb |
(ftp)(http) |
GFF |
| GSM838797_587_Pup_WPP_2d_CNS_B81CG2ABXX_TGACCA_4_pA_plus.gff.gz |
171.9 Kb |
(ftp)(http) |
GFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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