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Sample GSM851127 Query DataSets for GSM851127
Status Public on Feb 05, 2013
Title Mouse villus cell input DNA
Sample type SRA
Source name Mouse villus cell input DNA
Organism Mus musculus
Characteristics tissue: Mouse villus
antibody: none
type: input DNA
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 sonicated input DNA fragments
Data processing 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 SRX112512
BioSample SAMN00767700

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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