|
| Status |
Public on Jun 30, 2010 |
| Title |
Case 11 - wt (13058601) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Universal human reference RNA (UHRR) from Stratagene
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: reference RNA pool
|
| Biomaterial provider |
Stratagene
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
NA
|
| Label |
Cy5
|
| Label protocol |
Fluorescence-labeled cDNA was synthesized from extracted RNA by reverse transcription using ChipShot™ Direct Labeling System (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).
|
| |
|
| Channel 2 |
| Source name |
Fresh GIST tissue, without exon 11 deletion
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: fresh GIST tumor sample
genotype: wt
|
| Biomaterial provider |
Department of Surgery, Sahlgrenska University Hospital, Göteborg, Sweden
|
| Treatment protocol |
Fresh tumors were frozen with liquid nitrogen and homogenizated with Tirzol Reagent (Invitrogen Life Technologies).
|
| Growth protocol |
NA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from biopsies by homogenization with Trizol Reagent (Invitrogen Life Technologies, CA) using a TissueLyzer (Qiagen, MD) followed by RNA purification (RNeasy mini kit; Qiagen, Valencia, CA). The RNA quality was verified by gel electrophoresis. Fluorescence-labeled cDNA was synthesized from extracted RNA by reverse transcription using ChipShot™ Direct Labeling System (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).
|
| Label |
Cy3
|
| Label protocol |
Tumor RNA was labeled with Cy3-dCTP (Amersham BioSciences, Buckinghamshire, UK). Labeled cDNA probes were purified using Pronto! Plus Systems (Corning B.V, Schiphol, Netherlands).
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed in a Corning Hybridization Chamber during 17 hours in 42ºC water bath, followed by post-hybridization washes (Pronto! Plus Systems; Corning B.V, Schiphol, Netherlands).
|
| Scan protocol |
Microarrays were quantified in an Agilent microarray scanner (G2505B; Agilent Technologies, Palo Alto, CA) and image processing was carried out using Feature Extraction Software v7.5 (Agilent Technologies).
|
| Description |
Case 11. See Table 1 in Arne et al 2009.
|
| Data processing |
The microarray data was normalized using lowess normalization. No background correction was done.
|
| |
|
| Submission date |
Feb 09, 2009 |
| Last update date |
Dec 20, 2009 |
| Contact name |
Erik Kristiansson |
| E-mail(s) |
erik.kristiansson@chalmers.se
|
| Organization name |
Chalmers University of Technology
|
| Department |
Department of Mathematical Sciences
|
| Street address |
Chalmers Tvärgata 3
|
| City |
Göteborg |
| ZIP/Postal code |
412 96 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL5345 |
| Series (1) |
| GSE14755 |
Expression profiling of GIST: CD133 is associated with KIT exon 11 deletion, gastric location and poor prognosis |
|
