|
| Status |
Public on Aug 13, 2012 |
| Title |
HCT116.Parent.2 [expression] |
| Sample type |
RNA |
| |
|
| Source name |
HCT116 cultured cells wild-type for IDH1
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: wild-type
|
| Treatment protocol |
2,000,000 cells were plated to a 25cm2 flask and harvested after 48 hours for RNA isolation
|
| Growth protocol |
Cell lines were cultured in McCoy’s 5A Medium supplemented with 10% FBS. All cells were maintained in 5% CO2 at 37°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA isolation was performed using the RNeasy Kit (Qiagen) following the manufacturer's protocol
|
| Label |
Biotin
|
| Label protocol |
T7-based RNA amplication was performed on total RNA using the MessageAmp aRNA kit from Ambion (Austin, TX). For second round amplification, cDNA for each sample was in vitro transcribed (IVT) to biotin-labeled cRNA with the IVT labeling kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Fragmented cRNA and hybridization controls were hybridized to U133A GeneChips (Affymetrix) for 16 hours and then washed and stained according to the standard antibody amplification for eukaryotic targets protocol (Affymetrix)
|
| Scan protocol |
The stained arrays were scanned using an Affymetrix GeneChip Scanner 3000 according to the manufacturer's protocol
|
| Description |
HCT116 wild-type parent cells
|
| Data processing |
Data were RMA normalized using Expression Console (Affymetrix) Version 1.1. Detection was determined using MAS5.0 analysis, also conducted in Expression Console.
|
| |
|
| Submission date |
Aug 02, 2011 |
| Last update date |
Aug 13, 2012 |
| Contact name |
Benjamin G Barwick |
| E-mail(s) |
[email protected]
|
| Phone |
(404) 285-2964
|
| Organization name |
Emory University
|
| Department |
Hematology and Medical Oncology
|
| Lab |
Barwick Lab
|
| Street address |
1365 Clifton Rd. NE WCI-C 4th Floor Benches 36-37
|
| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (2) |
| GSE31126 |
DNA methylation alterations and transcriptional gene silencing induced by IDH1 R132H mutation [Affymetrix] |
| GSE31134 |
DNA methylation alterations and transcriptional gene silencing induced by IDH1 R132H mutation |
|
