|
| Status |
Public on Nov 06, 2013 |
| Title |
HCT116-Normoxia-3 |
| Sample type |
RNA |
| |
|
| Source name |
HCT116-Normoxia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
cell type: colon carcinoma
|
| Biomaterial provider |
ATCC: CCL-247
|
| Growth protocol |
Cells were grown adherent at 80% confluency on glass dishes that in contrast to plastic do not release oxygen. Growth medium: RPMI Media 1640- Invitrogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy Mini Kit (Qiagen) and quality assessed on an Agilent 2100 Bioanalyzer. 250 ng from each of 24 RNA samples (4 groups, 2 cell lines, triplicate)
|
| Label |
biotin
|
| Label protocol |
labeled using Illumina TotalPrep RNA Amplification kit (Ambion)
|
| |
|
| Hybridization protocol |
750ng of cRNA generated from amplification and labeling were hybridized to 2 Human HT-12 v4.0 BeadChips.
|
| Scan protocol |
The BeadChips were scanned on the Illumina iScan platform after washing and staining.
|
| Description |
Normoxia
|
| Data processing |
Data files were quantified in GenomeStudio Version 2011.1. All samples passed Illumina's sample dependent and independent quality control metrics with one sample having higher background and overall signal intensities resulting in lower detection calls relative to the other samples. This sample was included following normalization. Bead summary text files containing quality corrected median intensity values for each probe were loaded into the R statistical environment (v2.13.2). Data were normalized using the variance stabilizing method VSN as implemented by the beadarray package v2.2.0.
|
| |
|
| Submission date |
Oct 17, 2012 |
| Last update date |
Nov 06, 2013 |
| Contact name |
Nicholas J Harding |
| E-mail(s) |
nicholas.harding@oicr.on.ca
|
| Phone |
4167320720
|
| Organization name |
OICR
|
| Department |
Informatics and Biocomputing Platform
|
| Lab |
Boutros
|
| Street address |
101 College St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL10558 |
| Series (1) |
| GSE41666 |
Disulphide bond inhibitors in 2 cancer cell lines |
|
