|
|
| Status |
Public on Nov 19, 2009 |
| Title |
Caco-2-DS8235 |
| Sample type |
RNA |
| |
|
| Source name |
colorectal adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal adenocarcinoma
term: BTO:0000195
|
| Biomaterial provider |
ATCC;HTB-37
|
| Treatment protocol |
not applicable
|
| Growth protocol |
Followed vendor recommendations for growth protocol/media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At cell harvest, a subset of cells was stored at -20oC in RNALater. Total RNA from 5 X 10^6 cells were purified using Ribopure (Ambion) according to vendor recommended protocols. Total RNA quality was assessed on RNA 6000 Nano Chips (Agilent) using a Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
A Whole Transcript Sense Target Labeling Assay (Affymetrix) was used to reduce the rRNA, perform in vitro transcription (IVT) and create labeled sense strand DNA for hybridization to the arrays.
|
| |
|
| Hybridization protocol |
Hybridizations were carried out according the manufacturer (Affymetrix) protocol
|
| Scan protocol |
Affymterix Gene Chip Scanner 3000
|
| Description |
X_Hs_CACO2_E_080325_01_DS8235_W.CEL
|
| Data processing |
Intensity files from the scanned exon arrays were analyzed at the exon level (Affymetrix ExACT 1.2.1 software). Sample data were quantile normalized with PM-GCBG background correction and PLIER (Probe Logarithmic Intensity Error) summarized
Probe group file used for analysis: HuEx-1_0-st-v2.r2.pgf
|
| |
|
| Submission date |
Nov 18, 2009 |
| Last update date |
Apr 23, 2013 |
| Contact name |
ENCODE DCC |
| E-mail(s) |
encode-help@lists.stanford.edu
|
| Organization name |
ENCODE DCC
|
| Street address |
300 Pasteur Dr
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305-5120 |
| Country |
USA |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE19090 |
Exon arrays of ENCODE tier 1, tier 2 and tier 3 cell types |
|
