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Series GSE12241 Query DataSets for GSE12241
Status Public on Jul 25, 2008
Title Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Genome-wide maps of chromatin state (H3K4me3, H3K9me3, H3K27me3, H3K36me3, H4K20me3) in pluripotent and lineage-committed cells
We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.
Overall design Histone H3 or H4 tri-methylation ChIP-Seq in singlicate from murine embryonic stem (ES) cells, ES-derived neural precursor cells, and embryonic fibroblasts.
Contributor(s) Mikkelsen TS, Ku M, Lander ES, Bernstein BE
Citation(s) 17603471, 19946276
Submission date Jul 24, 2008
Last update date May 15, 2019
Contact name Tarjei S Mikkelsen
Organization name Broad Institute
Street address 7 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (21)
GSM307605 ESHyb_H3K4me3_ChIPSeq
GSM307606 ESHyb_H3K36me3_ChIPSeq
GSM307607 ESHyb_H3K9me3_ChIPSeq
SRA SRP000415
BioProject PRJNA113703

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE12241_RAW.tar 8.7 Gb (http)(custom) TAR (of TXT)
GSE12241_README.aligned.txt 404 b (ftp)(http) TXT
GSE12241_README.densities.txt 657 b (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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