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Sample GSM851123 Query DataSets for GSM851123
Status Public on Feb 05, 2013
Title H3K4me2 ChIP-Seq in Cdx2 KO mouse villus cells
Sample type SRA
Source name H3K4me2 ChIP-Seq in Cdx2 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 Cdx2KO mouse villus cells
Data processing H3K4me2_villus_Cdx2KO_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
SRA SRX112508
BioSample SAMN00767696

Supplementary file Size Download File type/resource
GSM851123.txt.gz 3.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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