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Status |
Public on Dec 31, 2010 |
Title |
breast cancer FA15 |
Sample type |
RNA |
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|
Source name |
breast cancer FNA biopsy, pre-treatment
|
Organism |
Homo sapiens |
Characteristics |
tissue: breast cancer FNA biopsy pcr.v.rd: pCR array.qc: Pass p53 status: MUT er positive vs negative by esr1 mrna gene expression (probe 205225_at): ERneg er positive vs negative by immunohistochemistry: ERpos age: 50 prechemo t: 2 prechemo tumor size: NA prechemo n: NA bmn.grade: 3
|
Treatment protocol |
Patients received neoadjuvant chemotherapy regimen with 5-Fluorouracil, Doxorubicin (Epirubicin) and Cyclophosphamide
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Extracted molecule |
total RNA |
Extraction protocol |
total RNA was extracted from the FNA specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).
|
Label |
biotin
|
Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).
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|
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Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.
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Scan protocol |
GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.
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Description |
Gene expression data from breast cancer FNA biopsy, pre-treatment Characteristics legend: pCR: pathologic complete response was defined as no residual invasive cancer in the breast and lymph nodes after preoperative chemotherapy. RD: residual disease was defined as any degree of invasive cancer that survived preoperative chemotherapy. Prechemo T and Prechemo N: were modified by TNM staging system in the American Joint Committee on Cancer Prechemo Tumor size: Clinical tumor size BMN.grade: were modified by Black's Nuclear Grade
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Data processing |
The data were normalized using dChip version 1.3 followed by logrithm-base-2 sc600 transformation. The dChip version 1.3 was used to calculate Model Based Expression Index (MBEI) values of the arrays using the digital standard microarray MDA-BCNorm.CEL and the probe sensitivity index file UTMDACC-BreastCancerNormalizer.psi as described in Hess, et. al, Pharmacogenomic Predictor of Sensitivity to Preoperative Chemotherapy With Paclitaxel and 5-Fluorouracil, Doxorubicin, and Cyclophosphamide in Breast Cancer, Journal of Clinical Oncology, 24 (26), 2006.
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Submission date |
Jun 02, 2010 |
Last update date |
Jun 06, 2022 |
Contact name |
TAKAYUKI IWAMOTO |
E-mail(s) |
[email protected]
|
Organization name |
UT MD Anderson
|
Department |
Breast medical Oncology
|
Street address |
1515 Holcombe Blvd
|
City |
Houston |
State/province |
TX |
ZIP/Postal code |
77030-4009 |
Country |
USA |
|
|
Platform ID |
GPL96 |
Series (1) |
GSE22093 |
Expression data from breast cancer FNA biopsies from patients |
|
Relations |
Reanalyzed by |
GSE205568 |