|
| Status |
Public on Mar 22, 2016 |
| Title |
C57BL/6J FAIRE HF Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
diet: High Fat - 16wk
|
| Treatment protocol |
mice were fed three regimen: 1) Con: 16wk of control diet, 2) HF: 16 wks of HF diet, or 3) Reversal: 8wk of HF diet followed by 8wk of control diet
|
| Growth protocol |
Livers were harvested from humanely euthanized mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were prepped according to the Illumina instructions for RNA-seq or DNA-seq
|
| |
|
| Library strategy |
FAIRE-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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.
RNA-seq: RNAs were extracted from livers using Trizol (Invitrogen). RNAs were prepared for sequencing using Illumina protocols and sequenced on the HiSeq 2500 (Illumina). The reads were aligned to the mm9 reference genome with Tophat using the RefSeq gene annotation for transcript reference. Deseq2 was used to identify differentially expressed transcripts from the RefSeq gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Deseq2 output
Supplementary_files_format_and_content: FAIRE-seq: narrowPeaks format
|
| |
|
| Submission date |
Dec 14, 2015 |
| 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) |
| GSE75984 |
Persistent chromatin modifications induced by high fat diet |
|
| Relations |
| BioSample |
SAMN04335412 |
| SRA |
SRX1480702 |
