|
| Status |
Public on Sep 17, 2013 |
| Title |
HT29 at 10 μM of 5-Aza, biological rep1 |
| Sample type |
RNA |
| |
|
| Source name |
HT29 treated with 10 μM of 5-Aza
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human colon cancer cell line
cell line: HT29
treatment: 10 μM of 5-Aza
|
| Treatment protocol |
Triplicate cultures of HT-29 cells were treated in the following three experimental groups: 1.) Vehicle (DMSO) alone or 0 µM 5-Aza-deoxycytidine (5-Aza); 2.) 5 µM 5-Aza; 3.) 10 µM 5-Aza
|
| Growth protocol |
HT-29 colon cancer cells were cultured as monolayers in 150 mm dishes in DMEM with 10% fetal bovine serum, 1% kanamycin, streptomycin-penicillin at 37 CO2 5% .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each monolayer was washed with PBS, scraped and centrifuged into a pellet. RNA was extracted from each pellet using Tri-Reagent according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
The biotinylated cRNA was hybridized on the Affymetrix hgu133 plus2.0 arrays. Gene chips were washed and stained using the Affymetrix GeneChip® Fluidics Station 450
|
| Scan protocol |
Gene chips were scanned using the Affymetrix GeneChip® Scanner 3000 7G
|
| Description |
RNA samples from human colon cancer HT29 cell line
|
| Data processing |
Gene expression intensities were initially extracted from the CEL files and proceeded with 75% percentile scalling and RMA normalization. Subsequently a filter step was applied to remove probes with one or more absence flags in a given group. The software we used for data normalization are GeneSpring GX (Agilent Inc) and R bioconductor package affy (v 1.14.2).
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| |
|
| Submission date |
Oct 05, 2012 |
| Last update date |
Sep 17, 2013 |
| Contact name |
Xiao Xu |
| E-mail(s) |
slowsmile820@gmail.com
|
| Organization name |
Stony Brook University BME
|
| Street address |
Stony Brook University
|
| City |
Stony Brook |
| State/province |
NY |
| ZIP/Postal code |
11794 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (2) |
| GSE41364 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine [Affymetrix] |
| GSE41588 |
Expression data for HT29 cells treated with 5-aza-deoxy-cytidine |
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