|
| Status |
Public on Jan 17, 2013 |
| Title |
OSC RNA-seq biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
OSC cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: OSC cells
sample type: PCR amplified cDNA (cellular polyA+ RNA)
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using QIAShredder (QIAGEN; cat.no. 79654) and RNeasy Mini Kit (QIAGEN; cat.no. 74106; including DNase I on column digestion) from 5-10 x 10^6 cells. 5ug total RNA was then processed as described before (S. Zhong et al., High-throughput illumina strand-specific RNA sequencing library preparation., Cold Spring Harbor protocols 2011, 940-9 (2011)) with minor adjustments. End-repair, dA-tailing and adapter ligation were performed with the NEBNext DNA Library Prep Reagent Set for Illumina (NEB, cat.no. E6000L) with proportionally reduced enzyme amounts to account for low RNA concentrations. Indexed library amplification was carried out using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PCR amplified cDNA (cellular polyA+ RNA)
|
| Data processing |
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) and bfast reconciling the outputs. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths.
Genome_build: dm3
Supplementary_files_format_and_content: Processed data files are in plain text. For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.
|
| |
|
| Submission date |
Sep 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Daniel Gerlach |
| E-mail(s) |
daniel.gerlach@boehringer-ingelheim.com
|
| Organization name |
Boehringer Ingelheim RCV GmbH & Co KG
|
| Department |
Global Computational Biology and Digital Sciences
|
| Street address |
Dr.-Boehringer-Gasse 5-11
|
| City |
Vienna |
| ZIP/Postal code |
1121 |
| Country |
Austria |
| |
|
| Platform ID |
GPL13304 |
| Series (1) |
| GSE40739 |
Genome-wide quantitative enhancer activity maps identified by STARR-seq |
|
| Relations |
| Reanalyzed by |
GSM3281486 |
| SRA |
SRX187087 |
| BioSample |
SAMN01176872 |
