|
| Status |
Public on Nov 25, 2010 |
| Title |
Colon FF D-1 |
| Sample type |
RNA |
| |
|
| Source name |
Fresh-frozen tissue, colon tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon tumor
fixation: FF
block age (at extraction in years): 1
biological replicate: rep-1
donor: F tumor
|
| Treatment protocol |
NA.
|
| Growth protocol |
NA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNEasy kit.
|
| Label |
biotin
|
| Label protocol |
Purified RNA was subjected to whole-transcriptome amplification using the WT-Ovation FFPE system. For RNA extracted from frozen or FFPE sections, 10 ng or 50 ng of input RNA, respectively, was used to generate amplified Ribo-SPIA product. All clean-up steps were performed with RNAClean magnetic beads (Agencourt Biosciences). Five micrograms of WT-Ovation product were used to fragment and label using the FL-Ovation Biotin V2 labeling module and labeled product was hybridized to Affymetrix Human U133 Plus 2.0 (Wilm’s and kidney quadsets) or U133Av2 (lung and colon quadsets) GeneChips following manufacturer’s recommendations (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized for 16-20 hr at 45C on GeneChip arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).
|
| Description |
LT_CN_FRTUM1
|
| Data processing |
The data were analyzed with Affymetrix Expression Console using RMA-sketch quantile as normalization method.
|
| |
|
| Submission date |
Dec 01, 2009 |
| Last update date |
Dec 01, 2009 |
| Contact name |
Elai Davicioni |
| E-mail(s) |
elai.davicioni@veracyte.com
|
| Organization name |
Veracyte, Inc
|
| Street address |
9725 Lusk Blvd
|
| City |
San Diego |
| State/province |
California |
| ZIP/Postal code |
92121 |
| Country |
USA |
| |
|
| Platform ID |
GPL571 |
| Series (1) |
| GSE19249 |
Quantitative Gene Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays |
|
