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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jul 06, 2008 |
Title |
Brain_H3K4me2_ChIPSeq |
Sample type |
SRA |
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Source name |
Whole brain
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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 |
SRX000585 |
BioSample |
SAMN02195370 |
Supplementary file |
Size |
Download |
File type/resource |
GSM281697_Brain.H3K4me2.aligned.txt.gz |
250.4 Mb |
(ftp)(http) |
TXT |
GSM281697_Brain.H3K4me2.densities.txt.gz |
279.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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