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Series GSE98724 Query DataSets for GSE98724
Status Public on Jan 11, 2018
Title Transcription factor-dependent ‘anti-repressive’ mammalian enhancers exclude H3K27me3 from extended genomic domains
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To define and assess the role of transcription factor binding at villus enhancers, we performed ATAC-seq and ChIP-seq.
We used RNA-sequencing to profile gene expression changes upon transcription factor loss. Loss of gene expression correlated with transcription factor-dependent enhancers and reveal the role of certain enhancers in H3K27me3 exclusion.
 
Overall design ATAC-seq and ChIP-seq (H3K4me1, H3K4me2, H3K27ac, H3K27me3, H3K9me3, H3K4me3, CDX2, HNF1A, PBRM1, RNA PolII, SMARCC1, CTCF, MED1 and KDM6A) analysis of isolated mouse intestinal differntiated villus epithelial cells. RNA-seq analysis of mouse intestinal differentiated villus epithelial cells.
 
Contributor(s) Saxena M, San Roman AK, O’Neill NK, Sulahian R, Jadhav U, Shivdasani RA
Citation(s) 29321178
Submission date May 09, 2017
Last update date Jul 25, 2021
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
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (47)
GSM2610627 Wild-type Villus CDX2 ChIP-seq biological rep1
GSM2610628 Wild-type Villus CDX2 ChIP-seq biological rep2
GSM2610629 Cdx2-/- Villus CDX2 ChIP-seq biological rep1
Relations
BioProject PRJNA386029
SRA SRP106735

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
GSE98724_Cdx2KO_ATAC.bw 341.7 Mb (ftp)(http) BW
GSE98724_RAW.tar 9.3 Gb (http)(custom) TAR (of BW)
GSE98724_RNASeq_Read_Counts_All_Samples.txt.gz 318.7 Kb (ftp)(http) TXT
GSE98724_WTVil_ATAC.bw 337.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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