|
| Status |
Public on Sep 01, 2021 |
| Title |
Breast cancer_BH0470-2 [re-analysis] |
| Sample type |
RNA |
| |
|
| Source name |
Breast cancer tumor tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast
age: 60
Stage: 2
ihc: HR-/HER2+
grade: 3
alive: Alive
relapse status: non-relapse
overall survival (years): 3.3
relapse free survival (years): 3.3
array_ssp1: HER2
array_ssp2: HER2
nano_ssp1: HER2
nano_ssp2: HER2
|
| Treatment protocol |
Breast cancer samples were prospectively collected during surgery. Cancerous breast tissues were snap-frozen and stored in liquid nitrogen at -80 °C with RNAlaterTM reagent (Qiagen, Germantown, MD) within 30 minutes after surgery. Frozen samples were cut into 1~2-mm thick slices, and slices with more than 90% of cancer content were selected for microarray experiment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). RNA was purified using RNeasy® mini kits (Qiagen, Valencia, CA) and RNA integration was checked by gel electrophoresis.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).
|
| Scan protocol |
GeneChips were scanned using a GeneChip Scanner 3000.
|
| Description |
re-analysis of GSM4392983
|
| Data processing |
Scanned images processed by GeneChip® Operating Software and Affymetrix’s Microarray Suite software to generate detection p values. The Robust Multichip Average (RMA) algorithm, which consisted three steps of background adjustment, quantile normalization, and final summarization, was applied for perfect match probe signals within the study.
|
| |
|
| Submission date |
Nov 27, 2020 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Chih-Cheng Chien |
| Organization name |
Sijhih Cathay General Hospital
|
| Street address |
No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist
|
| City |
New Taipei |
| ZIP/Postal code |
22174 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE162228 |
Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese breast cancer |
|
| Relations |
| Reanalysis of |
GSM4392983 |
