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| Status |
Public on Jun 23, 2016 |
| Title |
PH_WT_rep2_ChIPSeq |
| Sample type |
SRA |
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| Source name |
Embryo 16h-18h
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: WT
tissue: Embryo
age: 16-18
antibody: PH
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin prepared from Drosophila embryos was immunoprecipitated with specific antibodies and precipitated DNA was isolated (see mat and methods for details)
Libraries were prepared according to Illumina's instructions
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Mapping - For each ChIP-seq experiment, we mapped short reads to the appropriate reference genome using Bowtie by specifying ‘-a –m 1 -best -strata’ options. Our reference genomes included the heterochromatic fraction of chromosomes and non-assembled contigs, and any read that could be mapped to more than one genomic locus was filtered from further processing.
Peak finding – For PH MACS 1,4 has been used with standard parameters, with genome size set to dm. For H3K27me3, SICER has been used with 500bp windows, 2kb as gap and FDR at 10 %
Genome_build: dm³
Supplementary_files_format_and_content: bedgraph files were generated with custom scripts from raw aligned files, bed files were generated with MACS1.4 for PH and SICER for H3K27me3
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| Submission date |
Jun 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Bernd Schuettengruber |
| E-mail(s) |
bernd.schuttengruber@igh.cnrs.fr
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| Organization name |
Institute de Génétique Humaine
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| Lab |
Cavalli
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| Street address |
141, rue de la cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE60428 |
Cooperativity, specificity and evolutionary stability of Polycomb targeting in Drosophila |
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| Relations |
| BioSample |
SAMN05285450 |
| SRA |
SRX1872292 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2211687_PH2.bedgraph.gz |
39.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM2211687_PH2_peaks.bed.gz |
27.5 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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