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Sample GSM559083 Query DataSets for GSM559083
Status Public on Dec 01, 2010
Title 833_T_b
Sample type RNA
 
Source name mammary gland, tumor
Organism Canis lupus familiaris
Characteristics tissue: primary mammary carcinoma
tissue type: tumor
breed: Rottweiler
age in years: 10
tumor size (cm): 3
affected lymph node: inguinal
postoperative survival (months): 6
era: -
her-2: +
Extracted molecule total RNA
Extraction protocol Tumor specimens were macrodissected to ensure high tumor or normal gland cellularity, respectively, and only sections that contained 70% tumor or non-neoplastic mammary epithelial cells, respectively, were included in the study. Tissue sections were transferred into 300 μl of lysis buffer (NucleoSpin RNA; Macherey&Nagel, Dueren, Germany) and homogenized (Precellyse 24, Bertin Technology, France). mRNA was extracted and purified using a commercial system (NucleoSpin RNA; Macherey&Nagel, Germany).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol (One Cycle Target labeling protocol) from 2ug total RNA.
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Canine Genome 2.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Scanner G3000.
Description Dog 3
Data processing Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.4, Partek Inc., St. Louis, USA) and processed by the implemented gcRMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).
 
Submission date Jun 22, 2010
Last update date Dec 01, 2010
Contact name Dido Lenze
E-mail(s) dido.lenze@charite.de
Organization name Charité-Universitätsmedizin Berlin
Department Pathologie, Campus Benjamin Franklin
Street address Hindenburgdamm 30
City Berlin
ZIP/Postal code 12200
Country Germany
 
Platform ID GPL3738
Series (1)
GSE22516 Metastatic Cascade is Reflected in the Gene Expression of Metastatic Canine Mammary Carcinomas Similar to Human Breast Cancer

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 6.67184
AFFX-BioB-5_at 7.02411
AFFX-BioB-M_at 7.67481
AFFX-BioC-3_at 9.20049
AFFX-BioC-5_at 8.59403
AFFX-BioDn-3_at 11.6362
AFFX-BioDn-5_at 10.5778
AFFX-Cf_Actin_3_at 14.04
AFFX-Cf_Actin_5_s_at 14.14
AFFX-Cf_Actin_M_at 12.089
AFFX-Cf_AdrenRecpt_3_at 1.99453
AFFX-Cf_AdrenRecpt_5_at 1.90219
AFFX-Cf_AdrenRecpt_M_at 2.35294
AFFX-Cf_G-6-PDH_3_at 2.8041
AFFX-Cf_G-6-PDH_5_at 2.09785
AFFX-Cf_G-6-PDH_M_at 2.53725
AFFX-Cf_Gapdh_3_at 14.8202
AFFX-Cf_Gapdh_5_at 14.8896
AFFX-Cf_Gapdh_M_at 13.5285
AFFX-Cf_P450-2E1_3_s_at 2.87606

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM559083.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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