|
| Status |
Public on May 13, 2010 |
| Title |
E2F4 liver ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
liver hepatocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
sample: hepatocytes
chip antibody: E2F4
|
| Growth protocol |
Tissue samples were harvested from male C57BL/6J. Animals were provided with water and chow without restriction. Murine preadipocyte 3T3-L1 cells were induced to differentiate to mature adipocytes using a standard protocol (Goldfine et al. Diabetes 2006)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hepatocytes were harvested by direct perfusion of the liver in anaesthetized animals using PBS, followed by crosslinking with a 1% formaldehyde solution. The liver was then removed and crosslinked for another 10 minutes followed by neutralization with glycine. This cellular material was homogenized, washed and passed through a sucrose gradient to enrich for hepatocytes. These were rinsed with 1X PBS, pelleted, and either used directly in ChIP experiments, or frozen in liquid nitrogen for later use. Mouse cerebella were harvested from male C57BL/6J mice and crosslinked, homogenized, and neutralized in a similar manner. 3T3-L1 cells were cross linked for ten minutes and then quenched with glycine.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Chromatin IP against E2F4
|
| Data processing |
Alignment: ChIP-seq analysis of immunoprecipitated DNA was carried out using the standard Illumina protocols and analysis pipeline.
BED files: Peak files, the enrichment of genomic regions for protein binding was assessed relative to a set of control reads obtained by sequencing unenriched whole-genome DNA. Bound regions were identified using the MACS algorithm with a calculated alignable genome size of 2.107 Gbp and an enrichment p-value cutoff of 1e-6.
|
| |
|
| Submission date |
Jul 13, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Kenzie MacIsaac |
| E-mail(s) |
macisaac@mit.edu
|
| Phone |
617-253-2042
|
| Fax |
617-395-2661
|
| URL |
http://fraenkel.mit.edu
|
| Organization name |
MIT
|
| Street address |
77 Massachusetts Ave.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE17067 |
A quantitative model of transcription regulation reveals the role of non-conserved enhancers |
|
| Relations |
| SRA |
SRX019010 |
| BioSample |
SAMN00011114 |
