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Sample GSM559096 Query DataSets for GSM559096
Status Public on Dec 01, 2010
Title 1232_N
Sample type RNA
 
Source name mammary gland, normal
Organism Canis lupus familiaris
Characteristics tissue: mammary gland
tissue type: normal
breed: West Highland White Terrier
age in years: 16
era: na
her-2: na
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 10
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 8.43769
AFFX-BioB-5_at 8.42599
AFFX-BioB-M_at 9.19633
AFFX-BioC-3_at 10.6676
AFFX-BioC-5_at 9.8578
AFFX-BioDn-3_at 12.7085
AFFX-BioDn-5_at 12.0476
AFFX-Cf_Actin_3_at 14.1454
AFFX-Cf_Actin_5_s_at 14.9221
AFFX-Cf_Actin_M_at 12.9502
AFFX-Cf_AdrenRecpt_3_at 1.98524
AFFX-Cf_AdrenRecpt_5_at 1.86629
AFFX-Cf_AdrenRecpt_M_at 2.25763
AFFX-Cf_G-6-PDH_3_at 2.78284
AFFX-Cf_G-6-PDH_5_at 2.04162
AFFX-Cf_G-6-PDH_M_at 2.52158
AFFX-Cf_Gapdh_3_at 14.4629
AFFX-Cf_Gapdh_5_at 14.4434
AFFX-Cf_Gapdh_M_at 13.1426
AFFX-Cf_P450-2E1_3_s_at 2.93608

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM559096.CEL.gz 3.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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