|
| Status |
Public on Jan 01, 2013 |
| Title |
Input |
| Sample type |
SRA |
| |
|
| Source name |
Liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
tissue: Liver
time: ZT10
chip antibody: none (Input)
|
| Treatment protocol |
Mice were euthanized and livers were removed at ZT10, 5pm.
|
| Growth protocol |
10-12 week old male C57Bl/6 mice has been housed in regular 12h light/12h dark cycles on normal chow.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Liver samples were cross-linked with 1% formaldehyde, and used for ChIP with specififed antibody(ies).
Nuclei were lysed and sonicated. Protein-DNA complexes were isolated from lysates using antibodies, and DNA were extracted. For each condition, ChIP was performed on lysates from 4-5 different mice, and ChIPed DNA or input DNA samples were pooled for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Sequencing and alignment: Sequencing was done by the Functional Genomics Core at the University of Pennsylvania. Sequence reads were processed and mapped to the mouse genome (mm8) using ELAND pipeline. Before subsequent analysis, redundant reads in each genomic position were condenced into one to avoid possible PCR bias or each sample.
Peak Calling: Then two WT samples (WT and GFP) were pooled into one as single WT sample. Peak calling was performed by Homer with default parameters then 1rpm cut-off was applied, where maximum two reads were counted in WT samples due to the pooling, and one read were considered in NS-DADm sample.
Genome_build: mm8
Supplementary_files_format_and_content: Peak calling results for WT and NS-DADm samples in bed format.
|
| |
|
| Submission date |
Nov 27, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Hee-Woong Lim |
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Department |
Division of Biomedical Informatics
|
| Street address |
3333 Burnet Ave. MLC 7024
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE42540 |
Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo (ChIP-Seq) |
| GSE42541 |
Nuclear Receptor Corepressors are Required for the Histone Deacetylase Activity of HDAC3 In Vivo |
|
| Relations |
| SRA |
SRX206482 |
| BioSample |
SAMN01819849 |
