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| Status |
Public on Mar 27, 2014 |
| Title |
S2_ChIPseq_with_ecd |
| 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
chip antibody: anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory
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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 |
genomic DNA |
| Extraction protocol |
10^8 cells with and without treatment were harvested. Chromatin was sonicated with Tip sonicator (Omni Sonic Ruptor 250 Watt Ultrasonic Homogenizer) for 7 cycles (1 min on (duty cycle 30%, output 20%)) 1 min off) in 2 ml of Lysis buffer 3. The anti-EcR monoclonal antibody (DDA2.7) developed by C. Thummel in D. Hogness laboratory was obtained from the Developmental Studies Hybridoma Bank developed under the auspices of the NICHD and maintained by The University of Iowa, Department of Biology, Iowa City, IA 52242. 1 ml of chromatin was incubated with 3 μl of antibody (135 μg/ml) overnight. Chromatin and 25 μl of blocked Dynabeads Protein G (Invitrogen, cat. no. 10004D) were combined and incubated at 4° C for additional 2 hrs. 3 ng of material was used for library generation. Library was constructed following instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L). Library amplifcation was done using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
S2_ChIPseq_with_ecd_rep1
S2_ChIPseq_with_ecd_rep2
PCR amplified DNA
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| 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 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.
ChIP-seq peaks were called using STARR-seq pipeline using following parameters: -M 50 -W 1000 -D 600 -Z 1.67 -g dm3 -P 0.001
Genome_build: dm3
Supplementary_files_format_and_content: ChIP-Seq processed files supplement_ChIP_peaks_no_ecd.txt and supplement_ChIP_peaks_with_ecd.txt contain chr, summit, enrichment and p-values for called peaks.
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| Submission date |
Jul 31, 2013 |
| 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 |
SAMN02298432 |
| SRA |
SRX330270 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1199045_shlyueva_supplement_ChIP_peaks_with_ecd.txt.gz |
11.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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