NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM886577 Query DataSets for GSM886577
Status Public on Apr 15, 2014
Title Breast cancer 17
Sample type RNA
 
Source name Breast cancer fresh tissue
Organism Homo sapiens
Characteristics tissue: breast cancer tumor
histological type: IDC
age (y): 41
grade: 3
site: L
er (1= positive, 0=nagative): 0
pr (1= positive, 0= negative): 0
her2 (1=positive, 0=negative): 1
triple negative (1= yes, 0= no): 0
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.
City Jeddah
ZIP/Postal code 21589
Country Saudi Arabia
 
Platform ID GPL6244
Series (1)
GSE36295 Transcriptomic analysis of breast cancer

Data table header descriptions
ID_REF
VALUE GCRMA normalized value

Data table
ID_REF VALUE
7892501 4.01103
7892502 5.16681
7892503 4.47137
7892504 9.1048
7892505 2.64753
7892506 2.60394
7892507 4.81462
7892508 4.28574
7892509 10.4144
7892510 4.06121
7892511 1.89104
7892512 6.81563
7892513 2.88816
7892514 8.64008
7892515 8.19372
7892516 5.03464
7892517 5.37461
7892518 3.07033
7892519 4.20246
7892520 9.20641

Total number of rows: 33297

Table truncated, full table size 516 Kbytes.




Supplementary file Size Download File type/resource
GSM886577_TM-143-09R_HuGene-1_0-st-v1_.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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