|
| Status |
Public on Mar 20, 2012 |
| Title |
Breast cancer tumor OU-97 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer tumor
age: 60
clinical t stage: 2
lymph node status: positive
clinical stage: IIB
histological grade: 3
er status ihc: negative
pr status ihc: negative
her2 status fish: negative
pathologic response pcr ncr: pCR
|
| Treatment protocol |
Patients prospectively consented to a research biopsy by vacuum-assisted core-biopsy instrument (Mammotome 8G; HH Ethicon Endosurgery, Johnson and Johnson Company) under ultrasonographic guidance for histologic examination and gene expression analysis prior to any systemic therapy, and to the future assessment of pathologic response
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol (Invitrogen, Carlsbad, Calif) was used to extract RNA from core-needle tumor biopsy samples that were obtained with the Mammotome.
|
| Label |
biotin
|
| Label protocol |
RNA (50 ng) was subjected to the generation of second-strand combinational DNA (cDNA), and cRNA was amplified with a random primer (WT-Ovation FFPE RNA Amplification System V2; NuGEN, Cincinnati, Ohio). Next, the amplified cRNA was biotinylated and fragmented with the FL-Ovation cDNA Biotin Module V2 (NuGEN).
|
| |
|
| Hybridization protocol |
Following fragmentation, 5 ug of cRNA were hybridized overnight at 46C on Affymetrix U133 plus2.0 arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000.
|
| Data processing |
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.
|
| |
|
| Submission date |
Oct 05, 2011 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Shinzaburo Noguchi |
| E-mail(s) |
noguchi@onsurg.med.osaka-u.ac.jp
|
| Phone |
+81-6-6879-3772
|
| Fax |
+81-6-6879-3779
|
| Organization name |
Osaka University, Graduate School of Medicine
|
| Department |
Breast and Endocrine Surgery
|
| Street address |
2-2-E10 Yamada-oka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
565-0871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE32646 |
GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer |
|
| Relations |
| Reanalyzed by |
GSE205568 |
