|
| Status |
Public on May 19, 2011 |
| Title |
colorectal cancer sample AUS2_200_p1591 [exon-level] |
| Sample type |
RNA |
| |
|
| Source name |
Colorectal cancer patient
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectal cancer biopsy
tumor stage: 3
msi-status: NA
disease_free_survival_event: 2.75
disease_free_survival_years: 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For the colorectal cancer samples, total RNA was isolated from <30 mg tissue biopsies using the AllPrep DNA/RNA Mini kit (Qiagen), according to the manufacturer's protocol. For the normal colon mucosa samples, total RNA was isolated from <100 mg tissue biopsies using the Ambion RiboPure kit (Life Technologies), according to the manufacturer's protocol.
|
| Label |
biotin
|
| Label protocol |
Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).
|
| |
|
| Hybridization protocol |
Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix)
|
| Scan protocol |
Array scanning was performed according to the manufacturer's instruction (Affymetrix)
|
| Data processing |
For analysis at the exon level, raw data were processed (using a custom-made cdf-file; HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf) and analyzed for alternative splicing with the FIRMA algorithm (aroma.affymetrix). For gene-level analysis, raw data were processed with the RMA procedure using Expression Console (Affymetrix; gene-core analysis).
|
| |
|
| Submission date |
Apr 21, 2011 |
| Last update date |
Jul 01, 2011 |
| Contact name |
Anita Sveen |
| E-mail(s) |
anita.sveen@rr-research.no
|
| Organization name |
Institute for Cancer Research, Oslo University Hospital
|
| Department |
Department of Molecular Oncology
|
| Street address |
P.O.Box 4953, Nydalen
|
| City |
Oslo |
| ZIP/Postal code |
NO-0424 |
| Country |
Norway |
| |
|
| Platform ID |
GPL11028 |
| Series (2) |
| GSE24550 |
Exon level expression profiling of colorectal cancer tissue samples (validation sample series). |
| GSE24551 |
Exon level expression profiling of colorectal cancer tissue samples |
|
| Relations |
| Alternative to |
GSM712474 (gene-level) |
