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| Status |
Public on Oct 21, 2012 |
| Title |
ESC_H3K9me3 |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
strain: 129P2/Ola
cell type: mouse embryonic stem cells
antibody: H3K9me3 (Abcam ab8898)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For chromatin immunoprecipitation, for each sample, 1 x 106 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). Chromatin was sheared to mononucleosomal fragments. After IgG preclearance the sheared chromatin was incubated with 4 µg of either a H3K9ac (Abcam, ab4441), a H3K27ac (Abcam, ab4729), or a H3K9me3 (Abcam ab8898) antibody over night. After washes with sonication (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na-deoxycholate), high-salt- (50 mM Hepes pH 7.9, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate, 0.1% SDS), lithium- (20 mM Tris-HCl pH 8.0, 1mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and 10 mM Tris-HCl, chromatin was eluted from the protein G magnetic beads and the crosslink was reversed over night. After RNase A and proteinase K digestion, the DNA was purified and subsequently cloned into a multiplexed Illumina library according to standard protocols.
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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 |
For ChIP-seq, reads were aligned with Bowtie to the mouse mm9 genome build allowing up to two mismatches. Only unique hits were accepted. Sequenced 50 bp reads were mapped with Bowtie and subsequently clustered with MACS 55 implemented in the Genomatix software suite (Genomatix, Munich, Germany) using a p-value of 10-5.
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed
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| Submission date |
Sep 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Vladimir B Teif |
| E-mail(s) |
vteif@essex.ac.uk
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| Organization name |
University of Essex
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| Department |
School of Life Sciences
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| Street address |
Wivenhoe Park
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| City |
Colchester |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE40896 |
Genome-wide nucleosome positioning during embryonic stem cell development |
| GSE40951 |
Genome-wide nucleosome positioning during embryonic stem cell development [ChIP-Seq] |
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| Relations |
| SRA |
SRX187621 |
| BioSample |
SAMN01178496 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1005505_ESC_H3K9me3_peaks.bed.gz |
111.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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