|
| Status |
Public on May 04, 2020 |
| Title |
HSF1_ZT14_INPUT |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: liver
chip antibody: none
time point: ZT 14
|
| Growth protocol |
Mice were housed under a 12-h light/12-h dark regimen with food and water available ad libitum. ZT0 is defined as the time when the lights are turned on. Animals were housed for 3 weeks under the indicated photoperiods.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For the HSF1 ChIP-Seq, chromatin preparation and chromatin immunoprecipitation were performed as in Rey et al., PLoS Biol 2011. The HSF1 polyclonal antibody is from Stressgen (Enzo Life Sciences). For each IP, 5ul of HSF1 antibody was used with 250ul of pre-cleared chromatin.
Libraries for ultra-high throughput sequencing were prepared with the ChIP-Seq DNA sample kit (Illumina) as recommended by the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Input DNA
|
| Data processing |
Alignment: Sequence reads were aligned to the mouse genome (mm9) using BWA software
bigwig were produced using deeptools bamCoverage command with the following parameters: --centerReads --extendReads 37
HSF1peaks were analysed using Macs2 with default parameters with a p-value threshold below 0.001 and annotated with the closest gene using Chippeakanno R package.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, anannotated Macs2 peaks in txt format
|
| |
|
| Submission date |
May 04, 2020 |
| Last update date |
May 07, 2020 |
| Contact name |
Jonathan Aryeh Sobel |
| E-mail(s) |
jonathan.sobel@epfl.ch
|
| Organization name |
EPFL
|
| Department |
School of Life Sciences
|
| Lab |
Felix Naef Lab
|
| Street address |
EPFL SV IBI-SV UPNAE AAB 0 36 (Batiment AAB) Station 15
|
| City |
Lausanne |
| State/province |
Vaud |
| ZIP/Postal code |
CH-1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL9185 |
| Series (2) |
| GSE60430 |
Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver [DNase-seq, ChIP-seq] |
| GSE60578 |
Regulatory logic of the coupled diurnal and feeding cycles in the mouse liver |
|
| Relations |
| BioSample |
SAMN14827291 |
| SRA |
SRX8244938 |
