GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE70766 Query DataSets for GSE70766
Status Public on Sep 15, 2015
Title Distinct processes and transcriptional targets underlie CDX2 requirements in intestinal stem cells and differentiated villus cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary To define target genes of the intestine-restricted transcription factor (TF) CDX2 in intestinal stem cells, we performed chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq).
We used RNA-sequencing to profile gene expression changes during cell differentiation from mouse intestinal stem cells to mature villus cells, as well as genes perturbed in intestinal stem cells upon loss of Cdx2. We find thousands of genes that change in expression during cell differentiation, including known stem cell and mature markers. Upon loss of Cdx2, hundreds of genes are up and down-regulated in intestinal stem cells, some of which are also bound by CDX2 nearby and constitute candidate direct target genes.
Overall design CDX2 ChIP-Seq analysis of isolated mouse intestinal stem cells. RNA seq analysis of control mouse villus cells, control intestinal stem cells and Cdx2-deleted intestinal stem cells.
Web link
Contributor(s) San Roman AK, Tovaglieri A, Breault DT, Shivdasani RA
Citation(s) 26489894
Submission date Jul 10, 2015
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
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (11)
GSM1817693 Control Villus biological rep 1
GSM1817694 Control Villus biological rep 2
GSM1817695 Control Villus biological rep 3
BioProject PRJNA289517
SRA SRP060666

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
GSE70766_3prime-1000_ISC.gtf.gz 1.1 Mb (ftp)(http) GTF
GSE70766_Differential_expression.txt.gz 2.3 Mb (ftp)(http) TXT
GSE70766_Normalized_expression_Log2FPKM.txt.gz 714.1 Kb (ftp)(http) TXT
GSE70766_RAW.tar 938.6 Mb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap