|
| Status |
Public on Oct 06, 2022 |
| Title |
C646 + 1hr WO Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Schneider 2 (S2) cells
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R
developmental stage: Late embryonic stage
|
| Treatment protocol |
Experiments were conducted on cells at 80-90% confluency. Cells were resuspended in FBS-free media and incubated with 30 μM of C646 for 30 minutes, with or without a drug washout (WO) in media without C646 for either 1 hr or 4 hr.
|
| Growth protocol |
S2 cells were cultured at 25°C in Schneider's Drosophila medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco) and 1% Penicillin-Streptomycin (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA corresponding to 0.5-1 million control or drug treated S2 cells were homogenized in TRIzol LS (Ambion) and purified and concentrated using the RNeasy MinElute Cleanup kit (Qiagen) according to the manufacturer's instructions. RNA extractions were performed on three independent biological replicates.
RNA libraries were prepared from total RNA using the Illumina Stranded mRNA Prep kit and sequenced single-end (1 x 75 bp) on the Illumina NextSeq 2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
C646 + 1hr WO Rep 1
|
| Data processing |
RNA-seq reads were mapped to the Drosophila dm6 genome assembly using the STAR RNA-seq aligner with the default parameters. Coverage tracks of the mean RPKM signal from the three biological replicates were produced using deepTools. Reads mapping to the exons of genes were counted using featureCounts and differential gene expression analysis performed on the count data using the DESeq2 Bioconductor package.
Assembly: dm6
Supplementary files format and content: bigwig for coverage
|
| |
|
| Submission date |
Jun 07, 2022 |
| Last update date |
Oct 06, 2022 |
| Contact name |
Mattias Mannervik |
| E-mail(s) |
mattias.mannervik@su.se
|
| Organization name |
Stockholm University
|
| Department |
Dept. of Molecular Biosciences
|
| Street address |
Svante Arrhenius väg 20C
|
| City |
Stockholm |
| ZIP/Postal code |
106 91 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL30203 |
| Series (2) |
| GSE186723 |
p300/CBP sustains Polycomb silencing by non-enzymatic functions |
| GSE205627 |
p300/CBP sustains Polycomb silencing by non-enzymatic functions (RNA-seq on inhibitor-treated Drosophila S2 cells) |
|
| Relations |
| BioSample |
SAMN28901585 |
| SRA |
SRX15625083 |
