|
| Status |
Public on Feb 06, 2013 |
| Title |
EGFP_1 |
| Sample type |
SRA |
| |
|
| Source name |
S2-DRSC CELLS
|
| Organism |
Drosophila melanogaster |
| Characteristics |
RNAi: EGFP
replicate: 1
|
| Treatment protocol |
RNAi was carried out according to standard bathing protocols in 6-well plate format (Drosophila RNAi Screening Center, Harvard Medical School) by adding 15 µg of dsRNA to each well before platting S2-DRSC cells in serum free Schneider’s medium and starving cells for 30 min.
|
| Growth protocol |
S2-DRSC cells were grown in Schneider's Drosophila medium incl. 10% FCS at 25 degree celsius.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction from S2-DRSC cells was done using Trizol reagent according to manufacturer’s instruction for adherent cells (Invitrogen).
Illumina TruSeq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
tophat -p 13 -o tophat_alignment_BSSE-DSU-1902 -G Drosophila_melanogaster.BDGP5.25.64.cor.gtf --no-novel-juncs --no-novel-indels --no-coverage-search --no-closure-search --no-convert-bam /usr/local/paro/el5/bowtie/indexes/dm3_BDGPRelease5 BSSE-DSU-1902_CGATGTA_L007_R1_001.fastq.gz
htseq-count -q -s no ./tophat_alignment_BSSE-DSU-1902/accepted_hits.sam Drosophila_melanogaster.BDGP5.25.64.cor.gtf > 1902.counts
Genome_build: Release 5
Supplementary_files_format_and_content: htseq-count
|
| |
|
| Submission date |
Dec 28, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Tobias Kockmann |
| E-mail(s) |
[email protected]
|
| Organization name |
ETHZ
|
| Department |
D-BSSE
|
| Lab |
Paro
|
| Street address |
Mattenstr. 26
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE36450 |
The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila |
| GSE43180 |
Effects of FSH knockdown on gene expression |
|
| Relations |
| Reanalyzed by |
GSM3281959 |
| SRA |
SRX213159 |
| BioSample |
SAMN01881269 |
