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Series GSE83394 Query DataSets for GSE83394
Status Public on Jun 01, 2017
Title Chromatin access at specific genome sites distinguishes intestinal crypt populations with stem cell potential
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary To define differences in chormatin accessibility and histome modifications in intestinal stem and epithelial cells, we performed ATAC-seq and ChIP-seq.
We used RNA-sequencing to profile gene expression changes during intestinal stem cell differentiation into different cell types. We find that gene expression is correlated with the chromatin accessibility and reveals differences between intestinal stem cells types.
 
Overall design ATAC-seq, H3K4me1, H3K4me2 and H3K27ac ChIP-Seq analysis of isolated mouse intestinal stem cells and progenitor cells. RNA seq analysis of mouse intestinal stem, progenitor and differntiated cells.
 
Contributor(s) Jadhav U, Saxena M, O’Neill NK, Saadatpour A, Yuan G, Herbert Z, Shivdasani RA
Citation(s) 28648363
Submission date Jun 15, 2016
Last update date May 15, 2019
Contact name Ramesh Shivdasani
E-mail 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
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (49)
GSM2201101 Control Bmi1-GFP ATAC biological rep1
GSM2201102 Control Bmi1-GFP ATAC biological rep2
GSM2201103 Lgr5-GFP ISC ATAC biological rep1
Relations
BioProject PRJNA325805
SRA SRP076610

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE83394_Bmi1_ATAC.bw 256.7 Mb (ftp)(http) BW
GSE83394_Bmi1_Rad_24hr_ATAC.bw 237.2 Mb (ftp)(http) BW
GSE83394_Bmi1_Rad_36hr_ATAC.bw 243.1 Mb (ftp)(http) BW
GSE83394_CD274+69+_ATAC.bw 253.0 Mb (ftp)(http) BW
GSE83394_CD274+69+_DT-Treated_ATAC.bw 258.4 Mb (ftp)(http) BW
GSE83394_EP_ATAC.bw 254.2 Mb (ftp)(http) BW
GSE83394_Geo_Read_Counts_Table.txt.gz 731.2 Kb (ftp)(http) TXT
GSE83394_Lgr5_ATAC.bw 252.2 Mb (ftp)(http) BW
GSE83394_RAW.tar 2.4 Gb (http)(custom) TAR (of BW)
GSE83394_SP_ATAC.bw 247.0 Mb (ftp)(http) BW
Processed data is available on Series record
Processed data provided as supplementary file
Raw data are available in SRA

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