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Sample GSM559091 Query DataSets for GSM559091
Status Public on Dec 01, 2010
Title 2747_T_b
Sample type RNA
 
Source name mammary gland, tumor
Organism Canis lupus familiaris
Characteristics tissue: primary mammary carcinoma
tissue type: tumor
breed: West Highland White Terrier
age in years: 12
tumor size (cm): 1
affected lymph node: axillary
postoperative survival (months): 2
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 7
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 7.90077
AFFX-BioB-5_at 8.12575
AFFX-BioB-M_at 8.66835
AFFX-BioC-3_at 10.027
AFFX-BioC-5_at 9.49653
AFFX-BioDn-3_at 12.1066
AFFX-BioDn-5_at 11.2239
AFFX-Cf_Actin_3_at 14.1117
AFFX-Cf_Actin_5_s_at 13.886
AFFX-Cf_Actin_M_at 12.204
AFFX-Cf_AdrenRecpt_3_at 2.00246
AFFX-Cf_AdrenRecpt_5_at 1.91142
AFFX-Cf_AdrenRecpt_M_at 2.31379
AFFX-Cf_G-6-PDH_3_at 2.86381
AFFX-Cf_G-6-PDH_5_at 2.10891
AFFX-Cf_G-6-PDH_M_at 2.60631
AFFX-Cf_Gapdh_3_at 14.7686
AFFX-Cf_Gapdh_5_at 14.8528
AFFX-Cf_Gapdh_M_at 13.5789
AFFX-Cf_P450-2E1_3_s_at 2.97203

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM559091.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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