|
| Status |
Public on Jul 25, 2008 |
| Title |
NP_WCE_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
ES-derived neural precursor cells
|
| Organism |
Mus musculus |
| Characteristics |
Genotype: 129SvJae x C57BL/6
|
| Treatment protocol |
Described in Mikkelsen et al., Nature 2007
|
| Growth protocol |
Described in Mikkelsen et al., Nature 2007
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Whole cell extract (input DNA)
|
| Data processing |
Described in Mikkelsen et al., Nature 2007. 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).
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL9185 |
| Series (1) |
| GSE12241 |
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells |
|
| Relations |
| SRA |
SRX001940 |
| BioSample |
SAMN02195332 |
