|
| Status |
Public on Jul 17, 2014 |
| Title |
DBA/2J FAIRE Con Replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: DBA/2J
chip antibody: n/a
tissue: liver
diet: Control
|
| Treatment protocol |
Mice were fed control or high fat diet
|
| Growth protocol |
Livers were harvested from humanely euthanized mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepared according to Illumina instructions for RNA-seq or DNA-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FAIRE-seq
|
| Data processing |
FAIRE-seq: FAIRE was performed as previously described (Giresi et al., 2007). Isolated DNAs were barcoded and sequenced on the Illumina HiSeq 2500 to produced 100bp x 100bp paired-end reads. Reads were aligned to the mouse genome (version mm9, from the UCSC Genome Browser) using Bowtie2 with default options except for local alignment allowing for 1 mismatch in the seed sequence (Langmead and Salzberg, 2012). To assess the effect of sequence variation on the ability to map tags from DBA/2J liver to the mm9 reference genome, we generated a pseudo DBA/2J reference genome by substituting SNVs into the mm9 genome and performed the same analysis.
FAIRE-seq: narrowPeaks format
Genome_build: mm9
|
| |
|
| Submission date |
Mar 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Leung |
| Organization name |
Beckman Research Institute, City of Hope
|
| Department |
Diabetes/Cancer
|
| Lab |
Schones
|
| Street address |
1500 E. Duarte Rd
|
| City |
Duarte |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE55581 |
Diet-induced chromatin remodeling in mice livers |
|
| Relations |
| BioSample |
SAMN02673255 |
| SRA |
SRX481142 |
