|
| Status |
Public on Feb 05, 2013 |
| Title |
H3K4me2 ChIP-Seq in Cdx2-Cdx1 DKO mouse villus cells |
| Sample type |
SRA |
| |
|
| Source name |
H3K4me2 ChIP-Seq in Cdx2-Hnf4a D KO mouse villus cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mouse villus
antibody: Millipore 07-030, lots DAM1570816 and DAM1724042
type: ChIP DNA
strain: 129xC57BL6 mixed background
|
| Growth protocol |
for ChIP-seq experiments, Villus epithelium were isolated by incubating dissected jejunm tissues with 15mm EDTA and then mechanical disruption with gentle vortexing. Villi were collected atop a 70 um filter while smaller crypts and fragments of epithelium went through. Villi were then fixed in 1% Formaldehyde for 15 minutes at 4 degrees and allowed to warm to room temperature for 35 minutes before processing chromatin for ChIP. Genomic DNA was extracted by reverse crosslinking overnight in 1%SDS 0.1M NaHCO3 buffer and collected on PCR purification columns (Qiagen). For MNase preps, villi were collected in the same fashion but not fixed and instead treated with MNase. Both approaches have been described previously by the same contributors (PMID #s: 21402776 and 21074721)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries were constructed from pooled ChIP experiments totaling 10-20ng of DNA using Illumina's recommended protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
chromatin IP against H3K4me2 in Cdx2-Hnf4a D KO mouse villus cells
|
| Data processing |
H3K4me2_villus_Cdx2Hnf4aDKO_NPS_pe-5.txt; genome build: mm9
ChIP-Seq: ELAND mapping (mm9) + MACS.
|
| |
|
| Submission date |
Dec 20, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael P Verzi |
| Organization name |
Rutgers, the State University of New Jersey
|
| Department |
Genetics
|
| Lab |
Verzi
|
| Street address |
145 Bevier Road
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (2) |
| GSE34566 |
The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo (ChIP-seq data) |
| GSE34568 |
The transcription factor CDX2 maintains active enhancer in intestinal villus cells in vivo |
|
| Relations |
| SRA |
SRX112510 |
| BioSample |
SAMN00767698 |
