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Sample GSM1843530 Query DataSets for GSM1843530
Status Public on May 20, 2016
Title Wild-type Villus H3K27me3 ChIP-Seq rep 1
Sample type SRA
 
Source name Control mouse villus cells
Organism Mus musculus
Characteristics strain background: B6;129 mixed
genotype/variation: Eed+/+; Villin-CRE
cell type: Adult Epitheial cells; proximal 1/3 of intestine
chip antibody: H3K27me3 antibody (07-449, Millipore)
Treatment protocol Not injected with tamoxifen.
Extracted molecule genomic DNA
Extraction protocol Epithelium from proximal 1/3 of mouse intestine was isolated by incubation with 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Whole cell lysates were sonicated and incubated with 5 ug H3K27me3 antibody overnight (07-449, Millipore) for immunoprecipitation.
The ChIPseq DNA Sample Prep Kit (Illumina) was used to prepare libraries, and 50 bp single-end reads were sequenced on an Illumina Hi-Seq 2000 instrument.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Villus_H3K27me3_ChIP-seq
Villus_H3K27me3_ChIP
Data processing Alignment: ChIP-seq:bowtie. RNA-seq: Tophat, version 2.0.6
ChIP-Seq - peak calling: SICER, version 1.1
RNA-Seq - normalized and differential expression: Cufflinks, version 2.0.1; default setting; Cuffdiff was used with default settings and FDR cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq Tag Density bigwig file for visualizing aligned sequence tags
RNA-Seq: Differential expression table, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Control ISC, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
RNA-Seq: Differential expression tables, prepared using Cuffdiff with an FDR of 5%: contains average FPKM values for Control-villus and Eed-del Villus, as well as fold change in expression, P-values, and Q-values corrected for multiple hypothesis testing.
 
Submission date Aug 04, 2015
Last update date May 15, 2019
Contact name Ramesh Shivdasani
E-mail(s) ramesh_shivdasani@dfci.harvard.edu
Organization name Dana Farber Cancer Institute
Department Medical Oncology
Lab Shivdasani
Street address 450 Brookline Ave. Dana 720D
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL13112
Series (1)
GSE71713 Acquired tissue-specific promoter bivalency is a basis for PRC2 necessity in adult somatic cells
Relations
BioSample SAMN03956380
SRA SRX1132748

Supplementary file Size Download File type/resource
GSM1843530_Villus_H3K27me3_Rep1.bigwig 602.3 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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