|
| Status |
Public on Mar 21, 2013 |
| Title |
NUH.BT059 |
| Sample type |
RNA |
| |
|
| Source name |
Breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
ln status: LN+
er status: ER-
pgr status: PgR-
her2 status: He+
histological grade: G3
size (mm): 15
patient age: 61
histology: invasive ductal carcinoma
adjuvant treated? (0=no, 1=yes): 1
characteristics: endocrine? (0=no, 1=yes): 0
chemo? (0=no, 1=yes): 1
treatment type: CAFx6 cycles
dfs time: 5.83
dfs event (defined as any type of recurrence or death from breast cancer): 0
dmfs time: 5.83
dmfs event (defined as distant metastasis or death from breast cancer): 0
DSS time: 5.83
dss event (defined as death from breast cancer): 0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor specimens from the IJB and JRH we processed and profiled at the IJB (Christos Sotiriou). Specimens from the NUH were processed and profiled at the Genome Institute of Singapore. Total RNA was extracted from fozen tumor specimens by the Trizol method, cleaned on Qiagen RNeasy columns and analyzed for integrity on the Agilent Bioanalyzer.
|
| Label |
biotin
|
| Label protocol |
Five micrograms of total RNA was used to generate cRNA (target) according to the standard Affymetrix (3' IVT) protocol.
|
| |
|
| Hybridization protocol |
The standard Affymetrix GeneChip hyridization protocol was followed.
|
| Scan protocol |
The standard Affymetrix GeneChip scanning protocol was followed.
|
| Description |
SIN_BT059
included in study population (n=1,954) of Nagalla, et. al., Genome Biology, 2013
|
| Data processing |
The raw data were normalized by using MAS5 and batch-corrected by using Combat
|
| |
|
| Submission date |
Mar 18, 2013 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Jeff Chou |
| E-mail(s) |
jchou@wakehealth.edu
|
| Phone |
3367572617
|
| Organization name |
Atrium Health Wake Forest Baptist
|
| Street address |
Medical Center Blvd
|
| City |
Winston-Salem |
| State/province |
NC |
| ZIP/Postal code |
27157 |
| Country |
USA |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE45255 |
Expression Profiles of Breast Tumors from Singapore and Europe |
|
| Relations |
| Reanalyzed by |
GSE205568 |
