|
| Status |
Public on Feb 04, 2010 |
| Title |
BR_FNA_M316R1 |
| Sample type |
RNA |
| |
|
| Source name |
Sample ID -- 316, fine-needle aspiration, breast cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast cancer cells
age: 45
race: white
er_status: N
pcr_vs_rd: pCR
pr_status: N
tbefore: 4
nbefore: 3
bmngrd: 3
er: 0
her2 status: P
her2 ihc: 3
her2 fish: 4.59
histology: IDC + DCIS
treatment code: TH/FEC
treatments comments: Taxol/FEC+Herceptin: updated from(PACLITAXEL x 12, FEC x 4)
|
| Treatment protocol |
Patients received pretreatment fine-needle aspiration (FNA) of the primary breast tumor or ipsilateral axillary metastasis before starting chemotherapy as part of an ongoing pharmacogenomic marker discovery program. The aspiration was performed using a 23- or 25-gauge needle. Cells from two to three passes were collected in vials containing 1 mL RNA later solution (Ambion, Austin, TX) and stored at -80°C. FNA samples on average contain 80% neoplastic cells and contain little or no stromal cells or normal breast epithelium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FNA samples using the RNAeasy Kit (Qiagen, Valencia, CA). The amount and quality of RNA were assessed with DU-640 UV Spectrophotometer (Beckman Coulter, Fullerton, CA), and they were considered adequate for further analysis if the optical density 260/280 ratio was ≥1.8 and the total RNA yield was ≥ 1μg.
|
| Label |
biotin
|
| Label protocol |
biotin labeling
|
| |
|
| Hybridization protocol |
Affymetrix protocol
|
| Scan protocol |
Affymetrix protocol
|
| Description |
MAQC_Distribution_Status: MDA_R -- Not used
Please see the GSE20194_MDACC_Sample_Info.xls file on the GSE20194 Series record for additional information on the Sample characteristics
|
| Data processing |
MAS5
|
| |
|
| Submission date |
Feb 02, 2010 |
| Last update date |
Jun 06, 2022 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL96 |
| Series (2) |
| GSE16716 |
MicroArray Quality Control Phase II (MAQC-II) Project |
| GSE20194 |
MAQC-II Project: human breast cancer (BR) data set |
|
| Relations |
| Reanalyzed by |
GSE47561 |
| Reanalyzed by |
GSE205568 |
