NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM549238 Query DataSets for GSM549238
Status Public on Dec 31, 2010
Title breast cancer FA15
Sample type RNA
 
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
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).
 
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.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.
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
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.
 
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

Data table header descriptions
ID_REF
VALUE log2 sc600 transformed MBEI (Model Based Expression Index) values

Data table
ID_REF VALUE
1007_s_at 11.98794459
1053_at 9.672983843
117_at 7.230984774
121_at 10.47724936
1255_g_at 6.681168127
1294_at 9.352460369
1316_at 7.662211428
1320_at 4.622425958
1405_i_at 9.957738501
1431_at 6.169077039
1438_at 11.40460978
1487_at 8.992538952
1494_f_at 8.809469834
1598_g_at 11.52926724
160020_at 9.322830058
1729_at 8.565577352
1773_at 7.592785015
177_at 8.647754547
179_at 10.50207588
1861_at 8.386715553

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM549238.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap