|
| Status |
Public on Sep 12, 2013 |
| Title |
iPSC Rhbdd1 replicate 1 read counts |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Mus musculus |
| Characteristics |
cell type: iPSCs
strain: 129/BL6
|
| Growth protocol |
standard cell culture
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
submitter has not supplied any information
submitter has not supplied any information
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
induced pluripotent stem cells derived from MEFs by retorviral over-expression of Oct4, SOx2 and Klf4
|
| Data processing |
Two to seven 4C libraries were multiplexed and sequenced using the Illumina Genome Analyzer II to obtain 76 base pair (bp) reads or Illumina HIseq-2000 to obtain 100 bp reads.
The resultant reads were mapped to the mouse genome using Bowtie software (Langmead et al., 2009). Only reads that aligned to a unique position in the genome with no more than two sequence mismatches were retained for further analysis.
Reads that were successfully aligned to the genome were then remapped to the 736,199 unique HindIII sites along the genome (with respect to the 50bp upstream and downstream of the site) by matching their respective loci.
Genome_build: MM9
Supplementary_files_format_and_content: bedGraph-formatted files contain unqiue HindIII loci and associated 4C-seq read counts
|
| |
|
| Submission date |
Aug 20, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kathrin Plath |
| Organization name |
UCLA
|
| Street address |
615 Charles E. Young Drive South
|
| City |
Los Angeles |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE50029 |
Long-range chromatin contacts reveal a role for the pluripotency and Polycomb networks in genome organization |
|
| Relations |
| BioSample |
SAMN02319337 |
| SRA |
SRX337306 |
