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| 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.
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| |
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| 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 |
http://www.sciencedirect.com/science/article/pii/S2213671115002684
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| |
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| 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 |
| 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 |
| |
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| Platforms (2) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
|
| Samples (11)
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| Relations |
| BioProject |
PRJNA289517 |
| SRA |
SRP060666 |
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