|
| Status |
Public on Feb 24, 2012 |
| Title |
mouse colon4 |
| Sample type |
RNA |
| |
|
| Source name |
colonic SEMFs
|
| Organism |
Mus musculus |
| Characteristics |
cell type: subepithelial myofibroblasts
strain: C57BL6/J
|
| Growth protocol |
Intestinal SEMFs were cultured under published conditions. Human cancer cells were grafted subcutaneousely in combination with murine ISEMFs and grown in immunodeficient NOD/SCID mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard 3' IVT EXPRESS Affymetrix protocol from 0.1 ug total RNA (GENE CHIP 3' IVT EXPRESS User Manual, P/N702646 REV8, Affymetrix)
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip MOUSE Genome 430 2.0 Arrays or HUMAN Genome U133 plus2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the AFFYMETRIX GENE CHIP SCANNER 3000.
|
| Description |
Gene expression data from colonic SEMFs
|
| Data processing |
Microarray expression: RMA (bioconductor) with custom CDFs for background elimination and normalization in adddition to array normalization using Cluster
|
| |
|
| Submission date |
Feb 28, 2011 |
| Last update date |
Feb 24, 2012 |
| Contact name |
Janghee Woo |
| E-mail(s) |
janghee_woo@hms.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Street address |
44 Binney st.
|
| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE27564 |
Gene expression profiles of subepithelial myofibroblasts from mouse ileum or colon, implanted together with human cancer cells in mouse xenografts |
|
