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| Status |
Public on Jan 04, 2013 |
| Title |
PH_mitotic_S2-PH_ChIPSeq |
| Sample type |
SRA |
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| Source name |
S2 cell line
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: S2 experssing biotin-PH
chip antibody: none (streptavidin-coated beads used to pulldown biotinlyated PH)
facs sorting antibody: H3S10p
cell cycle profile: mitotic
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| Treatment protocol |
for mitotic samples S2 or S2-PH cells were treated with 350ng/ml (880nM) colchicine for 15hrs.
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| Growth protocol |
Drosophila S2 cells were grown in ESF921 medium (Expression Systems) at 27°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine. Cells were stained with antibodies to either anti-H3S10p (colchicine-treated cells) or anti-H3 (asynchronous cultures) that were either FITC-conjugated or treated with a FITC-conjugated secondary antibody and FACS sorted to collect FITC positive cells. Nuclear lysates were sonicated to generate 300-600 bp DNA fragments. Chromatin was incubated overnight with antibody against PSC at 4°C (S2 cells) or without antibody (S2-PH cells). Chromatin was precipitated with streptavidin-coated beads for 2 hours at 4°C. After washing and eluting from beads the crosslinking was reversed and DNA was isolated. Eluted DNA and input DNA was sheared with a Bioruptor (Diagenode) to give ~180bp fragments. Libraries were generated by the BioMicroCenter (MIT) using the SPRI-works system.
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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 |
Alignment: Sequenced reads were aligned to the D. melanogaster genome (dm3) using Bowtie 1.1.2 (Langmead, B. et al., 2009) with the paramters -n 2 -m 1 --best --strata through Galaxy (Blankenberg, D. et al., 2010; Goecks, J. et al., 2010; Giardine, B. et al., 2005).
Peaks: peak detection was performed using the Model-Based Analysis of ChIP-Seq (MACS, version 1.0.1) through Galaxy using --tsize 36, --gsize 120000000 --bw 200 --nomodel --shiftsize 100. Peaks were filtered to retain peaks with a false discovery rate of 5% or below for all samples except for mitotic PH. Peaks on chromosome U and Uextra were removed.
Genome_build: dm3
Supplementary_files_format_and_content: Wig files were generated using MACS (version 1.0.1) and represent shifted tag counts for every 10bp. Wig files were normalzed by reads per million (RPM). Bed files contain a score that is given by -10*LOG10(pvalue).
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| Submission date |
May 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicole Follmer |
| E-mail(s) |
nfollmer@hms.harvard.edu
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| Organization name |
Harvard University
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| Street address |
16 Divinity Avenue
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
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| Platform ID |
GPL13304 |
| Series (1) |
| GSE38166 |
Polycomb Group proteins are retained at specific sites on chromatin in mitosis |
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| Relations |
| SRA |
SRX149197 |
| BioSample |
SAMN00997872 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM936122_PH_mitotic_S2-PH_ChIPSeq.bed.gz |
2.4 Kb |
(ftp)(http) |
BED |
| GSM936122_PH_mitotic_S2-PH_ChIPSeq.wig.gz |
34.6 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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