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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 06, 2008 |
| Title |
ES_H3K4me2_ChIPSeq |
| Sample type |
SRA |
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| Source name |
Embyonic stem cells (V6.5)
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| Organism |
Mus musculus |
| Characteristics |
Chromatin IP against H3K4me2
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| Growth protocol |
ES cells were cultured under standard conditions in the presence of LIF; NPCs were derived dy directed differentiation in the presence of Fgf2 (see Meissner et al., 2008)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Described in Mikkelsen et al., Nature 2007. Briefly, chromatin was fixed in 1% formaldehyde, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using Illumina Genome Analyzers as recommended by the manufacturer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Antibody: H3K4me2
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| Data processing |
Described in Meissner et al, 2008. Briefly, sequence reads from each IP experiment were aligned to the mouse reference genome (mm8), and all uniquely aligned reads (within >2 mismatches) were kept. Read densities were computed by counting the number of reads (extended to 300 bp) overlapping each position in the genome (at 25bp resolution).
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| Submission date |
Apr 14, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Tarjei S Mikkelsen |
| Organization name |
Broad Institute
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| Street address |
7 Cambridge Center
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL9185 |
| Series (1) |
| GSE11172 |
Genome-wide chromatin state maps of ES cells, ES-derived neural progenitor cells and brain tissue |
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| Relations |
| SRA |
SRX000582 |
| BioSample |
SAMN02195367 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM281694_ES.H3K4me2.aligned.txt.gz |
104.2 Mb |
(ftp)(http) |
TXT |
| GSM281694_ES.H3K4me2.densities.txt.gz |
263.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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