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| Status |
Public on Mar 27, 2014 |
| Title |
OSC_STARRseq_with_ecd_rep1 |
| Sample type |
SRA |
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| Source name |
OSC cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: OSC 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 |
Genomic DNA (source: embryos of the sequenced strain: y; cn bw sp) was isolated, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PCR amplified cDNA (STARR-seq transcript)
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| Data processing |
Library strategy: STARR-Seq
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 |
| BioSample |
SAMN02699967 |
| SRA |
SRX501037 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1357056_OSC_STARRseq_with_ecd_rep1.peaks.txt.gz |
296.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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