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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 28, 2008 |
| Title |
BIV1_H3K4me3_ChIPSeq |
| Sample type |
genomic |
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| Source name |
B lymphocyte-derived cell line BIV1
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| Organism |
Mus musculus |
| Characteristics |
Doxycycline induced Oct4, Klf4, c-Myc, Sox2 lentivirus
Antibody: H3K4me3 (Abcam ab8580)
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| Growth protocol |
MCV6, MCV8, MCV8.1 and BIV1 were cultured under standard mouse ES cell contitions in the prescence of LIF (see Mikkelsen, 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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| Description |
Antibody: H3K4me3 (Abcam ab8580)
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| Data processing |
Described in Mikkelsen 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 05, 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 |
GPL6693 |
| Series (1) |
| GSE11074 |
Chromatin state maps (H3K4me3 and H3K27me3) from partially and fully reprogrammed mouse cell lines |
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| Relations |
| SRA |
SRX000419 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM279940_BIV1.H3K4me3.aligned.txt.gz |
229.2 Mb |
(ftp)(http) |
TXT |
| GSM279940_BIV1.H3K4me3.densities.txt.gz |
279.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
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