|
| Status |
Public on Feb 22, 2019 |
| Title |
TN1021 |
| Sample type |
RNA |
| |
|
| Source name |
Bulk Tumor Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
lymph node: NA
grade: III
age: 73
death: yes
recurrence: yes
tumor size: 12
patient: mcgill.gq.31
|
| Treatment protocol |
All tissues were snap-frozen in O.C.T. Tissue-Tek Compound within 30 minutes of removal.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was then extracted from these sections using the AllPrep Mini kit (Qiagen). RNA quality was assessed using an Agilent Bioanalyzer
|
| Label |
biotin
|
| Label protocol |
Sense-strand cDNA was synthesized from 250ng of total RNA using the Ambion WT Expression Kit according to the manufacturer instructions (Life Technologies Corporation). The cDNA was fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer instructions (Affymetrix)
|
| |
|
| Hybridization protocol |
The fragmented and labeled DNA target was hybridized on GeneChip Human Gene 1.0 ST Array (Affymetrix) and incubated at 450C in the Genechip Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer's instructions (Affymetrix).
|
| Scan protocol |
The microarrays were scanned on a GeneChip scanner 3000 (Affymetrix) using the standard Affymetrix protocol.
|
| Description |
Gene expression from patient mcgill.gq.31
|
| Data processing |
Used Brainarray CDF package (hugene10sthsentrezgcdf_19.0.0)- Duplicate arrays were averaged. For genes with multiple probes, the probe with the highest IQR was chosen.
|
| |
|
| Submission date |
Oct 17, 2016 |
| Last update date |
Feb 22, 2019 |
| Contact name |
Benjamin Haibe-Kains |
| E-mail(s) |
[email protected]
|
| Phone |
+14165818626
|
| Organization name |
Princess Margaret Cancer Centre
|
| Department |
Princess Margaret Research
|
| Lab |
Bioinformatics and Computational Genomics
|
| Street address |
610 University Avenue
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 2M9 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20171 |
| Series (1) |
| GSE88847 |
Gene expression profiles of TN breast tumors |
|
