|
| Status |
Public on Feb 05, 2016 |
| Title |
Caco-2 Control-2 |
| Sample type |
RNA |
| |
|
| Source name |
medium alone
|
| Organism |
Homo sapiens |
| Characteristics |
Caco-2: human, Caucasian, colon, adenocarcinoma
|
| Biomaterial provider |
ECACC
|
| Treatment protocol |
Caco-2 cells were grown in 100-mm culture dishes to 3 days post-confluence in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics. Cells were washed twice with HBSS (Sigma) and incubated for 24 h in DTS medium containing DMEM, L-glutamine, transferrin and sodium selenite before treatment with the different conditions.
|
| Growth protocol |
Caco-2 cells were grown in culture flasks in DMEM (Sigma) containing 10% FCS, L-glutamine and antibiotics.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with an RNeasy kit (Qiagen) and included a DNAse I step (Qiagen). Poly (A)+ RNA was purified using an Oligotex mRNA mini kit (Qiagen).
|
| Label |
Biotin
|
| Label protocol |
Fragmented and biotin-labelled cRNA was synthesized from 1 ug purified mRNA using the One-Cycle Target Labeling Kit (Affymetrix) according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner.
|
| Description |
Caco-2 cells were treated with Salmonella enteritidis strains S1400 or EAV9 or recombinant flagellin, and their gene expression profile was compared to non-stimulated cells.
|
| Data processing |
Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA, p-values were adjusted using the Benjamini-Hochberg method.
|
| |
|
| Submission date |
Aug 24, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Denise Kelly |
| E-mail(s) |
[email protected]
|
| Phone |
+44 1224 716648
|
| Organization name |
University of Aberdeen
|
| Lab |
Gut Immunology Group
|
| Street address |
Institute of Medical Sciences
|
| City |
Aberdeen |
| ZIP/Postal code |
AB25 2ZD |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE8896 |
Flagellin-mediated effects of Salmonella enteritidis on gene expression in intestinal epithelial cells |
|
| Relations |
| Reanalyzed by |
GSE119087 |
