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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 20, 2013 |
| Title |
wt_H3K4me3 |
| Sample type |
SRA |
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| Source name |
Dnmt1+/+_MEFs_H3K4me3
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| Organism |
Mus musculus |
| Characteristics |
strain/cell line background: PMID 17311920
cell type: Mouse embryonic fibroblasts (MEFs)
genotype/variation: wild type; Dnmt1+/+
chip antibody: H3K4me3
chip antibody vendor: Millipore
chip antibody cat. #: 07-473
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| Growth protocol |
Mouse embryonic fibroblasts were cultured under standard conditions
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native ChIP was performed as described previously (Eskeland et al, 2010, Mol Cell, 38: 452-464) with the following adaptations. Protein-A coated Dynabeads (Invitrogen) were used throughout. Chromatin was digested with 25U of Mnase (micrococcal nuclease)(Worthington) for exactly 10min at room temperature. Following immunoprecipitation beads were washed three times for 10 min at 4°C in N-ChIP wash buffer (150mM NaCl; 10mM Tris pH8; 2mM EDTA; 1% NP40; 1% sodium deoxycholate w/v). Controls for N-ChIP experiments included a species matched IgG to control for background, negative and positive genomic regions to show specificity, and the use of input DNA to control for technical variations between cell lines or treatments. Antibodies were tested by western blot for recognition of histone-sized proteins only and by specific enrichment at positive control regions by N-ChIP. Enrichments were measured by qPCR.
Libraries were prepared according to Illumina's instructions by Ambry Genetics (Aliso Viejo, CA, USA)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
Sample 3
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| Data processing |
Base calling was performed as standard by Ambry Genetics (Aliso Viejo, CA, USA)
Reads were mapped to the mm9 build of the mouse genome using the bowtie short read aligner. Where a read mapped to a number of potential locations, only the best hit was retained (in terms of the number of mismatches and their qualities; as specified by the bowtie '–best' parameter
BEDTools was used to count the number of mapped reads that overlap genomic windows. This was outputted as a BedGraph
Genome_build: mm9
Supplementary_files_format_and_content: BedGraph files containing count data. Columns: chromosome; start coordinate of genomic window; stop coordinate of genomic window; number of mapped reads that overlap this window (windows with less than 5 overlapping windows are not shown)
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| Submission date |
Feb 19, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
James P Reddington |
| Organization name |
EMBL
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| Street address |
Meyerhofstrasse 1
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| City |
Heidelberg |
| ZIP/Postal code |
69115 Heidelberg |
| Country |
Germany |
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| Platform ID |
GPL11002 |
| Series (2) |
| GSE44278 |
Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of polycomb-target genes |
| GSE44393 |
Chip-seq for H3K27me3 and H3K4me3 in DNA methylation deficient mouse embryonic fibroblasts |
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| Relations |
| SRA |
SRX243598 |
| BioSample |
SAMN01923799 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1084282_wt_k4_profile_thresh5.bedGraph.gz |
21.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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