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| Status |
Public on Mar 27, 2014 |
| Title |
S2_RNAseq_with_ecd_rep2 |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
agent: ecdysone
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| Treatment protocol |
For all experiments cells were treated with ecdysone. The final concentration of ecdysone was 41 μM (10 mg of 20-hydroxyecdysone (Sigma; cat. no. H5142) per 500 ml of growth medium). After 24 hrs incubation with the hormone, cells were harvested.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PCR amplified cDNA (cellular polyA+ RNA)
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| Data processing |
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-Seq:
Reads were mapped to the dm3 genome using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa) excluding chrU, chrUextra, and chrM. For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
RNA-seq:
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: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input (log2-scale) at the summit, and the p-value. For the RNA-seq data we report 3 different gene identifiers and the RPKM value for each gene.
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| Submission date |
Mar 25, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daria Shlyueva |
| E-mail(s) |
daria.shlyueva@imp.ac.at
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| Organization name |
IMP
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| Lab |
Stark lab
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| Street address |
Dr. Bohr-gasse,7
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE47691 |
Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin |
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| Relations |
| Reanalyzed by |
GSM3285534 |
| BioSample |
SAMN02699964 |
| SRA |
SRX501034 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1357053_S2_RNAseq_with_ecd_rep2.rpkm.txt.gz |
163.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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