|
| Status |
Public on Oct 21, 2019 |
| Title |
DL8sc: DEX_ZT12 control REP1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: male
tissue: liver
treatment: 12 wk control Diet (Research Diet, D12329)
chip antibody: GR (Santa Cruz, sc-1004X)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Uhlenhaut et al. 2012). Briefly, 100 mg of frozen liver was minced and Dounce homogenated in 0.7 mg/mL DSG crosslinker and 1% Formaldheyde. Nuclei were isolated and chromatin sonicated to a 1-0.1 kb size by using Diagenode Bioruptor Plus. Sheared chromatin was then immunoprecipitated with specific antibodies.
Libraries from ChIP DNA and chromatin input were prepared by use of KAPA Hyperprep Kit (Kapa Biosystems, KK8504), Illumina compatible adapters were synthesized by IDT (Integrated DNA Technologies) and used at a final concentration of 68 nM. Adapted ligated libraries were size selected (360-610 bp) in a Pippin Gel station (Sage Science) using 2% dye free gels (Sage Science, CDF2010). Libraries concentration was estimated by Real Time PCR, with KAPA Library Quantification Kit (Kapa Biosystems, KK4873). Quality of the libraries was evaluated by use of the Agilent High Sensitivity DNA Kit (Agilent) in a 2100 Bioanalyzer (Agilent).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Mapping against mm9 mouse genome using bwa 7.12
Duplicate removal using samtools v2.4.0 and Downsampling
Peak calling with macs2 version 2.1.1
IP efficiency normalization
Create normalized peak universe
Genome_build: mm9
Supplementary_files_format_and_content: broadpeak and gappedPeak files were produced using macs2 representing GR peaks
|
| |
|
| Submission date |
Sep 25, 2019 |
| Last update date |
Oct 22, 2019 |
| Contact name |
Nina Henriette Uhlenhaut |
| E-mail(s) |
henriette.uhlenhaut@helmholtz-muenchen.de
|
| Organization name |
HelmholtzZentrum München - IDC
|
| Department |
Molecular Endocrinology
|
| Lab |
Uhlenhaut IDC
|
| Street address |
Ingolstädter Landstraße 1, Neuherberg
|
| City |
Munich |
| State/province |
Bavaria |
| ZIP/Postal code |
D-85764 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE108690 |
Cistromic reprogramming of the diurnal glucocorticoid hormone response by high fat diet |
| GSE137978 |
GR cistromes reprogramming by High Fat Diet [ChIP-seq: GR DEX] |
|
| Relations |
| BioSample |
SAMN12839254 |
| SRA |
SRX6902803 |
