|
| Status |
Public on Jan 27, 2016 |
| Title |
Input_MINT4 |
| Sample type |
SRA |
| |
|
| Source name |
Liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: none
treatment: OCA (10mg/kg/day)
strain: C57BL/6
gender: male
|
| Treatment protocol |
Male mice were treated daily by oral gavage for 7 days with OCA/INT-747 (10mg/kg/day) or vehicle (1% methyl cellulose).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei foxated with Formaldehyde/DSG, and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the instructions accompanyindg the SOLiD ChIP-seq kit for library preparation. Libraries were sequenced on the SOLiD 5500 WG following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Data processing |
Sequencing reads were mapped against the reference genome (mm9 assembly, NCBI37) using BWA package ( mem –t 7 –c 100 –M –R ).
Peaks were called using MACS 1.4 package (p 4, nomodel, nolambda, shiftsize=150) with each respective input as background
Wig files were constructed with custom perl script counts on extended reads on 50bp intervals
Genome_build: mm9
Supplementary_files_format_and_content: .wig.gz WIG files, scores represent read counts over 50bp intervals
Supplementary_files_format_and_content: .bed.gz Peak and Summit Intervals
|
| |
|
| Submission date |
Sep 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jose Miguel Ramos Pittol |
| E-mail(s) |
Jose.Ramos-Pittol@uibk.ac.at
|
| Organization name |
University of Innsbruck
|
| Department |
Institute of Biochemistry
|
| Street address |
Innrain 80-82
|
| City |
Innsbruck |
| ZIP/Postal code |
6020 |
| Country |
Austria |
| |
|
| Platform ID |
GPL16790 |
| Series (1) |
| GSE73624 |
Gene expression profiling and TF occupancy upon treatment with the FXR agonist obeticholic acid |
|
| Relations |
| BioSample |
SAMN04123809 |
| SRA |
SRX1297372 |
