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| Status |
Public on Mar 27, 2014 |
| Title |
S2_DHSseq_no_ecd_24hrs_rep2 |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell type: S2 cells
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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 |
5-7 10^7 cells were harvested. DNase treatment was done as in (L. Cappabianca, H. Thomassin, R. Pictet, T. Grange, Genomic footprinting using nucleases., Methods in molecular biology (Clifton, N.J.) 119, 427-42 (1999)). For size selection (~120bp) a sucrose gradient was emplyed (SW TI40, 30000rpm, 16h). 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 |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
PCR amplified DNaseI digested chromatin
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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.
DNase-Hypersensitivity
Reads were mapped to the dm3 genome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -) excluding chrU, chrUextra, and chrM. We estimated the enrichment and p-values for specific genomic regions using the cDNA and the input together with a hypergeometric test. To call peaks we also used MACS14 with default parameters and an FDR cutoff of 5%.
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. The DHS-seq peaks are directly taken from the MACS output. 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 |
Jun 06, 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 |
SAMN02191710 |
| SRA |
SRX297097 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1154838_S2_DHSseq_no_ecd_rep2.peaks.txt.gz |
122.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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