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| Status |
Public on Sep 21, 2018 |
| Title |
Input – H3K27Ac |
| Sample type |
SRA |
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| Source name |
HapES cells (AN3-12)
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| Organism |
Mus musculus |
| Characteristics |
antibody: None
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| Growth protocol |
Haploid ES cells were grown in standard ES cell medium with serum and LIF. ES cell medium contains of 450 ml DMEM (Sigma D1152); 75 ml FCS (Invitrogen); 5,5 ml P/S (Sigma P0781); 5,5 ml NEAA (Sigma M7145); 5,5 ml LGlu (Sigma G7513); 5,5 ml NaPyr (Sigma S8636); 0,55 ml bME Merck 805740 (dilute 10 l bME in 2.85 ml PBS for a 1000x stock); and ESGRO Millipore ESG1107 (according to instructions by the manufacturer).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina NEBNext kit
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP was essentially performed as described previously (Mohn et al., 2008). Briefly, after trypsinization and quenching 25 million Hap ES cells were washed once in PBS before fixing for 7 min by addition of formaldehyde to a final concentration of 1%. Crosslinking was then quenched by addition of 2.5 M glycine (0.125 M final concentration) and cells were then incubated on ice. Crosslinked cells were spun at 600 3 g for 5 min, nuclei were prepared by consecutive washes with Rinse 1 buffer (final: 50 mM HEPES pH 8.0, 140 mM NaCl, 10% glycerol, 0.5% NP40, 0.25% Triton X100, 1 mM EDTA) followed by Rinse 2 buffer (final: 10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl). Pellets were resuspended in 2 ml total volume of Sonication buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8 with protease inhibitors complete mini (Roche)) and then sonicated with a Covaris E220 sonicator (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 15 minutes). ChIP was perfomed in ChIP buffer (final: 50 mM HEPES/KOH pH 7.5, 300 mM NaCl , 1 mM EDTA, 1 % Triton X100, 0.1 % DOC, 0.1% SDS) with the indicated antibody.
The reads are aligned with Bowtie2 (standard parameter).
MACS (1.4) is used for peak calling of ATAC, H3K4me3, H3K27ac. Broad peaks of H3K27me3 are called with SICER (W1000, G3000).
Genome_build: mm10
Supplementary_files_format_and_content: Standard BED files of MACS and SICER
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| Submission date |
Sep 20, 2018 |
| Last update date |
Sep 24, 2018 |
| Contact name |
Thomas Rainer Burkard |
| E-mail(s) |
thomas.burkard@imba.oeaw.ac.at
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| Organization name |
IMBA
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| Street address |
Dr. Bohrgasse 7
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE84089 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets [ATAC-Seq, ChIP-Seq] |
| GSE84090 |
An inducible and reversible embryonic stem cell biobank reveals functional genomic pathways and disease targets |
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| Relations |
| BioSample |
SAMN10095490 |
| SRA |
SRX4720602 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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