|
| Status |
Public on May 17, 2011 |
| Title |
Untreated, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
CCD-18Co, untreated
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CCD-18Co
cell type: colon fibroblasts
treatment: none
|
| Treatment protocol |
Colon fibroblasts CCD-18Co were stimulated with SHH (1 ug/ml) for 72 h.
|
| Growth protocol |
Colon fibroblasts were cultured in media plus 0.1% BSA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Qiagen RNeasy kit.
|
| Label |
biotin
|
| Label protocol |
The method for preparation of cRNA was provided by Affymetrix. Briefly, 5 ug of total RNA was converted into double-stranded cDNA using a cDNA synthesis kit SuperScript Choice and a T7-(dT)24 oligomer primer. Double-stranded cDNA was purified on an affinity resin and ethanol precipitation. Following second-strand cDNA synthesis, labeled cRNA was generated using a T7 RNA polymerase and biotin-labeled nucleotide in an in vitro transcription reaction (Enzo Diagnostics). The labeled cRNA was purified on an affinity resin.
|
| |
|
| Hybridization protocol |
The method for hybridization of the arrays was provided by Affymetrix. Twenty micrograms of cRNA was fragmented and then hybridized to the arrays at 45°C for 19 hours in a rotisserie oven set at 60 rpm. Arrays were washed and stained in a Fluidics station.
|
| Scan protocol |
The method for array scanning was provided by Affymetrix. Arrays were scanned on an Affymetrix scanner.
|
| Data processing |
Data analysis was performed using the Affymetrix GeneChip Analysis software.
|
| |
|
| Submission date |
May 16, 2011 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Weiwei Chen |
| E-mail(s) |
weiweic@gene.com
|
| Organization name |
Genentech
|
| Street address |
1st DNA Way
|
| City |
SSF |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE29316 |
Expression data from colon fibroblasts treated with Sonic hedgehog homolog (SHH) |
|
| Relations |
| Reanalyzed by |
GSE86362 |
