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Sample GSM2201125 Query DataSets for GSM2201125
Status Public on Jun 01, 2017
Title Secretory Progenitors H3K27Ac ChIP-seq biological rep1
Sample type SRA
Source name mouse secretory progenitor cells
Organism Mus musculus
Characteristics strain: B6;129 mixed background
cell type: Adult Epitheial cells; proximal 1/3 of intestine
genotype: Atoh1 F/F
Treatment protocol Mice were injected with 48 mg/kg DBZ (notch inhibitor) at 0 hours, again at 12 hours, and sacrificed at 38 hours.
Growth protocol Crypts from the proximal 1/3 of mouse small intestines were isolated by scraping off villi and incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were snap-frozen in liquid nitrogen and pooled for subsequent ChIP analysis.
Extracted molecule genomic DNA
Extraction protocol Whole cell lysates were sonicated and incubated with 5 ug H3K27Ac antibody overnight (39135, Active MOtif) for immunoprecipitation.
The ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Description Secretory Progenitors H3K27Ac ChIP-seq biological rep1
Data processing Alignment: ATAC-seq and ChIP-seq:bowtie2. RNA-seq: Tophat, version 2.0.6
ATAC-seq peak calling: MACS, version 1.4
RNA-Seq - Read counts were normalized using Deseq2 with defalut parameters and further used for calculating differntial expression (q<0.05).
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChiP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with normalized gene expression (RPKM values) for all cell types
Submission date Jun 15, 2016
Last update date May 15, 2019
Contact name Ramesh Shivdasani
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 GPL19057
Series (1)
GSE83394 Dynamic Reorganization of Chromatin Accessibility Signatures during Dedifferentiation of Secretory Precursors into Lgr5+ Intestinal Stem Cells
BioSample SAMN05254256
SRA SRX1847662

Supplementary file Size Download File type/resource 694.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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