|
| Status |
Public on May 05, 2016 |
| Title |
wild-type total-RNA-seq biol rep 2 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type total-RNA-seq
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genetic cross: Oregon R
time: 74 ± 2 hours post egg laying
tissue: whole larvae (n ≈ 30)
|
| Growth protocol |
Larvae and pupae were cultured on molasses and agar at room temperature (24 ± 1°C). For pre-pupal collections, third instar larvae were transferred to vials.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Larvae were collected and washed with water at 74 ± 2 hours post egg laying. Larvae were then crushed in TRIzol and stored at -80°C. TRIzol extracted RNA was DNased with Ambion Turbo DNase.
Brown prepupae were collected and washed with water at < 12 hours post puparium formation. Prepupae were then crushed in TRIzol and stored at -80°C. TRIzol extracted RNA was DNased with Ambion Turbo DNase.
Illumina TruSeq RNA sample preparation kit v2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: gene_exp_eg_total.diff.gz
Oregon R_2 / EG004_TGACCA_L004
|
| Data processing |
base-calling: CASAVA v.1.8.2
alignment: TopHat v2.0.8 with Bowtie v2.1.0 and Samtools v0.1.19
analysis of differential expression: Cufflinks v2.0.2
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Cufflinks differential expression (.diff) files for FPKMs. Median two-quartile wild-type normalized bedgraph files and non-normalized bedgraph files for inspecting mapped reads in genome browsers.
|
| |
|
| Submission date |
May 04, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Eric L Garcia |
| E-mail(s) |
[email protected]
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Lineberger Comprehensive Cancer Center
|
| Lab |
Greg Matera
|
| Street address |
3344 Genome Science Bldg
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE81121 |
Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for Spinal Muscular Atrophy |
|
| Relations |
| Reanalyzed by |
GSM3279018 |
| BioSample |
SAMN04943423 |
| SRA |
SRX1743080 |
