|
| Status |
Public on May 11, 2011 |
| Title |
LBJ103 |
| Sample type |
RNA |
| |
|
| Source name |
breast cancer, sample LBJ/IN/GEI-LBJ103
|
| Organism |
Homo sapiens |
| Characteristics |
sample id: LBJ103
source: LBJ/IN/GEI
age_years: 63.0
er_status_ihc: P
pr_status_ihc: P
her2_status: N
clinical_t_stage: T3
clinical_nodal_status: N0
clinical_ajcc_stage: IIB
grade: 2
pathologic_response_pcr_rd: RD
pathologic_response_rcb_class: RCB-II
drfs_1_event_0_censored: 0
drfs_even_time_years: 3.08555783709788
type_taxane: Taxol
esr1_status: P
erbb2_status: N
set_class: SET-Low
chemosensitivity_prediction: Rx Insensitive
ggi_class: High
pam50_class: LumB
dlda30_prediction: RD
rcb_0_i_prediction: RCB-II/III
tissue: breast cancer tumor
|
| Treatment protocol |
Patients prospectively consented to a research biopsy by fine needle aspiration (FNA) or core biopsy (CBX) prior to any systemic therapy, and to the future assessment of pathologic response and/or survival endpoints
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tissue using Qiagen Rneasy columns
|
| Label |
biotin
|
| Label protocol |
A single-round T7 amplification was used to generate biotin-labeled cRNA for hybridization. At least 1 ug of RNA is required for cRNA synthesis.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized overnight at 46C on Affymetrix U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the diagnostic-grade Affymetrix scanner 3000DX
|
| Data processing |
Probe intensities were quantified with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. CEL files were normalized using global scaling with a trimmed mean target intensity of each array arbitrarily set to 600 using the MAS5 algorithm from the simpleaffy package (http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html).
|
| |
|
| Submission date |
Nov 01, 2010 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Christos Hatzis |
| E-mail(s) |
christos@nuverabio.com
|
| Phone |
781-938-3830
|
| URL |
http://www.nuverabio.com
|
| Organization name |
Nuvera Biosciences
|
| Street address |
400 West Cummings Park, Suite 5350
|
| City |
Woburn |
| State/province |
MA |
| ZIP/Postal code |
01801 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE25065 |
Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer |
| GSE25066 |
Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer |
|
| Relations |
| Reanalyzed by |
GSE205568 |
