|
| Status |
Public on Oct 13, 2012 |
| Title |
Enterocytes, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
mouse intestinal epithelial differentiated cells (enterocytes from conditional Atoh1 knockout)
|
| Organism |
Mus musculus |
| Characteristics |
background strain: C57BL/6
tissue: proximal intestinal epithelium
cell type: differentiated villus cells
genotype/variation: Atoh1 knockout
|
| Treatment protocol |
Tamoxifen (1mg/day for 5 days) was used to induce intestinal epithelial conditional knockout of Atoh1 and wait for 5 days to generate pure enterocytes in villus compartment
|
| Growth protocol |
intestinal epithelial cells from 4 to 6 weeks old mice
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
According to manufacturer's instructions (Affymetrix)
|
| Scan protocol |
According to manufacturer's instructions (Affymetrix)
|
| Description |
Gene expression data from Atoh1 knockout villus cells (Enterocytes)
|
| Data processing |
RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).
The 2 data sets (Lgr5(hi) and Enterocyte) were generated at separate time and batch correction was performed using Combat.
|
| |
|
| Submission date |
Oct 12, 2012 |
| Last update date |
Oct 13, 2012 |
| Contact name |
Amit Sinha |
| E-mail(s) |
[email protected]
|
| Phone |
617-582-7579
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Pediatric Oncology
|
| Lab |
Armstrong Lab
|
| Street address |
44 Binney St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02135 |
| Country |
USA |
| |
|
| Platform ID |
GPL8321 |
| Series (2) |
| GSE41541 |
Expression data from mouse proximal intestinal epithelial Lgr5(hi) stem cells and differentiated villus cells (enterocytes from Atoh1 conditional knockout) |
| GSE41543 |
DOT1L-mediated H3K79 methylation in chromatin is dispensable for Wnt pathway-specific and other intestinal epithelial functions |
|
