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Sample GSM317980 Query DataSets for GSM317980
Status Public on Dec 08, 2011
Title ER-negative placebo-treated patient 45
Sample type RNA
 
Source name Primary Breast cancer
Organism Homo sapiens
Characteristics histology: ductal
ER_status (0 - negarive, 1 - positive): 0
HER2_status (0 - negarive, 1 - positive): 1
treatment (1 - placebo, 2- tamoxifen): 1
Treatment protocol Excised tumor specimens were formalin fixed paraffin embedeed in a routine process.
Extracted molecule total RNA
Extraction protocol Tumor areas were identified by ER immunostaining with a hematoxylin counter stain. Total RNA was isolated from 3 to 5 five μn unstained sections using the Ambion RecoverAll™ Total Nucleic Acid Isolation Kit (Applied Biosystems, Foster City, CA) and quantified using UV absorption on a spectrophotometer (NanoDrop® ND-1000). 100-200 nanograms of total RNA were converted to cDNA and amplified using a commercial service provided by Rubicon Genomics, Inc. (Ann Arbor, Mi), using the TransPlex™ Whole Transcriptome Amplification (WTA) kit.
Label Cy3
Label protocol 3 μg of the WTA product were labeled with a fluorescent dye (Cy3) using a direct chemical labeling method (ULS™ Labeling Kit with Cy3 for Agilent Gene Expression Arrays, Kreatech Biotechnology, Amsterdam, The Netherlands)
 
Hybridization protocol After the labeling procedure, the amplified cDNA was purified with the KREA pure columns (Kreatech Biotechnology, Amsterdam, The Netherlands) to remove the dye in excess and was then fragmented using the Affymetrix fragmentation buffer provided with the GeneChip® Sample Cleanup Module Kit (Affymetrix, Santa Clara, CA). Finally, the cDNA was purified with the Clean-up columns, provided as well with the GeneChip® Sample Cleanup Module Kit, an added to the Hybridization Cocktail. The cocktail was then subjected to an overnight pre-hybridization to an used Affymetrix Genechip U133 2.0 Plus. The day after, 900 ng of the unbound labeled cDNA mix removed from the chip were processed as raccomanded by the manufacturer and hybridized to the Agilent Whole Human Genome (4 X 44 k) array. The hybridization was performed at 65 °C for 17 hours at a rotation of 10 revolutions per minute.
Scan protocol The slides were scanned using a DNA Microarray Scanner ( Agilent Technologies, Santa Clara, CA) and features were extracted using Agilent’s Feature Extraction Software (v 9.5.3.1).
Description n/a
Data processing Single channel hybridization intensity data were compiled using commercial software (Partek Genomic Suite, St Louis, Missouri). After quantile normalization, genes with mean intensity below 500 were filtred out. Data were log2 transformed for statistical analysis.
 
Submission date Sep 04, 2008
Last update date Dec 08, 2011
Contact name Soonmuyung Paik
Organization name NSABP Foundation
Department Pathology
Street address 1307 Federal Street, Suite 303
City Pittsburgh
State/province PA
ZIP/Postal code 15212
Country USA
 
Platform ID GPL6480
Series (1)
GSE12665 Gene expression profiling of invasive breast cancer events from the tamoxifen prevention trial

Data table header descriptions
ID_REF
VALUE Quantile normalization and log transformation

Data table
ID_REF VALUE
(+)E1A_r60_1 3.6923699378967
(+)E1A_r60_3 7.2844200134277
(+)E1A_r60_a104 5.7416400909424
(+)E1A_r60_a107 6.6336898803711
(+)E1A_r60_a135 6.438099861145
(+)E1A_r60_a20 8.4778003692627
(+)E1A_r60_a22 10.517900466919
(+)E1A_r60_a97 3.5771698951721
(+)E1A_r60_n11 5.6573801040649
(+)E1A_r60_n9 3.6509199142456
(-)3xSLv1 3.6123199462891
A_23_P100001 6.0290498733521
A_23_P100011 7.9621500968933
A_23_P100022 8.1140899658203
A_23_P100056 4.1694397926331
A_23_P100074 3.7688500881195
A_23_P100092 4.9602298736572
A_23_P100103 9.28600025177
A_23_P100111 10.715700149536
A_23_P100127 3.8966000080109

Total number of rows: 41056

Table truncated, full table size 1144 Kbytes.




Supplementary file Size Download File type/resource
GSM317980.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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