tissue: breast cancer tumor histological type: IDC age (y): 51 grade: 3 site: R er (1= positive, 0=nagative): 0 pr (1= positive, 0= negative): 0 her2 (1=positive, 0=negative): 0 triple negative (1= yes, 0= no): 1
Extracted molecule
total RNA
Extraction protocol
RNA samples for amplification with the Pico kit were isolated from fresh tissues using the RNeasy Micro Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA amplifications were carried out using Nugen Pico WTA amplification system according to the manufacturers’ suggestions followed by an additional amplification step using Nugen Exon Module.
Label
biotin
Label protocol
1ng total RNA was used as input for the Pico amplification and 4ug of amplified cDNA was used for Exon Module amplification. cDNA amplification products were fragmented and labeled with biotin using the NuGEN FL module, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit. And washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.
Hybridization protocol
standard Affymetrix protocol
Scan protocol
standard Affymetrix protocol
Description
Fresh Tissue
Data processing
The data were analyzed with Partek GS 6.5 and GCRMA as normalization method.
Submission date
Mar 06, 2012
Last update date
Apr 15, 2014
Contact name
Manikandan Jayapal
Organization name
King Abdulaziz University
Street address
King Fahd Medical Research Center | King Abdulaziz University | PO BOX 80216, Jeddah 21589. KSA.
