|
| Status |
Public on Mar 20, 2012 |
| Title |
CW-2 |
| Sample type |
RNA |
| |
|
| Source name |
RIKEN
|
| Organism |
Homo sapiens |
| Characteristics |
primary site: large_intestine
histology: carcinoma
|
| Treatment protocol |
None
|
| Growth protocol |
Cells lines were cultured following growth recommendations from the cell line source vendors. Cells were incubated at 37 ºC at 5% CO2 until 70% confluency was reached. Pellets were harvested 48 hours post media change, flash frozen, and stored at -80 ºC until nucleic acid extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from frozen cell pellets, containing an average cell count of 4.5 million cells, via Trizol (Invitrogen) extraction following the manufacturers instructions. Samples were quantified using both the Nanodrop 8000 spectrophotometer (ThermoScientific) and via Agilent 2100 Bioanalyzer.
|
| Label |
Biotin
|
| Label protocol |
The Affymetrix One-Cycle Target labeling assay was used to synthesize hybridization target using 1 mg of total RNA. Labeled cRNA hybridization target was produced using a 3-day, semi-automated workflow
|
| |
|
| Hybridization protocol |
Fragmentation of the biotin-labeled cRNA prepared the sample for hybridization on the GeneChip Human U133 2.0 (PN 900467). The washing and staining was performed on the GeneChip Fluidics station using standard Affymetrix protocols outlined in the Expression Analysis Technical Manual, 2001, Affymetrix.
|
| Scan protocol |
The GeneChip® Scanner 3000 was used for scanning the arrays.
|
| Description |
Gene expression data from the CCLE
|
| Data processing |
The data were analyzed with 2.14.0, using the packages affyio_1.22.0 and affy_1.32.0, and RMA as normalization method. rma() was used with default options (normalize=TRUE, background=TRUE) and with the package hgu133plus2hsentrezgcdf_15.0.0 from Brainarray for the CDF file.
|
| |
|
| Submission date |
Mar 06, 2012 |
| Last update date |
Sep 01, 2016 |
| Contact name |
Nicolas Stransky |
| E-mail(s) |
stransky@broadinstitute.org
|
| URL |
http://www.broadinstitute.org/ccle
|
| Organization name |
Broad Institute
|
| Department |
Cancer Program
|
| Lab |
Levi Garraway
|
| Street address |
7 Cambridge center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL15308 |
| Series (2) |
| GSE36133 |
Expression data from the Cancer Cell Line Encyclopedia (CCLE) |
| GSE36139 |
SNP and Expression data from the Cancer Cell Line Encyclopedia (CCLE) |
|
| Relations |
| Reanalyzed by |
GSE86362 |
