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Sample GSM520203 Query DataSets for GSM520203
Status Public on Dec 01, 2010
Title 825_T
Sample type RNA
 
Source name canine mammary carcinoma
Organism Canis lupus familiaris
Characteristics breed: Bobtail
age in years: 10
histologic grade: Grade III
tumor size (cm): 3
affected lymph node: inguinal
postoperative survival (months): 6
era: negative
her-2: +
Extracted molecule total RNA
Extraction protocol Tissue specimens were snap frozen in liquid nitrogen within 15 minutes after resection and stored at -80ºC until further use. Macrodissection was performed on all tumor specimens to ensure high tumor cellularity. Only sections with more than 70% carcinoma cells were included in the study as shown by digital image analysis (Scanscope T3, Aperio, Vista, USA; Zeiss Axiovision, Jena, Germany). For mRNA isolation, tissue sections were transferred into 300 µl of lysis buffer (NucleoSpin RNA XS; Macherey&Nagel, Dueren, Germany) and homogenized (Precellyse 24, Bertin Technology, France). RNA was extracted and purified using a commercial system (NucleoSpin RNA XS; Macherey&Nagel, Düren, Germany). The RNA quality was controlled using the BioAnalyzer (Agilent Technologies, USA) and only high quality RNA (RIN>8) was used for microarray analyses. Affymetrix GeneChip hybridization (Canine Genome 2.0 Array) was performed with 2 µg total RNA according to the manufacturer’s recommendations.
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 n/a
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 Mar 10, 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)
GSE20718 Metastatic Canine Mammary Carcinomas

Data table header descriptions
ID_REF
VALUE normalized log2 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 7.26084
AFFX-BioB-5_at 7.2019
AFFX-BioB-M_at 8.05231
AFFX-BioC-3_at 9.3369
AFFX-BioC-5_at 8.67121
AFFX-BioDn-3_at 11.5966
AFFX-BioDn-5_at 10.9492
AFFX-Cf_Actin_3_at 14.1954
AFFX-Cf_Actin_5_s_at 14.5005
AFFX-Cf_Actin_M_at 12.5577
AFFX-Cf_AdrenRecpt_3_at 1.91147
AFFX-Cf_AdrenRecpt_5_at 1.8693
AFFX-Cf_AdrenRecpt_M_at 2.28081
AFFX-Cf_G-6-PDH_3_at 2.87307
AFFX-Cf_G-6-PDH_5_at 2.02463
AFFX-Cf_G-6-PDH_M_at 2.78914
AFFX-Cf_Gapdh_3_at 14.8924
AFFX-Cf_Gapdh_5_at 14.7189
AFFX-Cf_Gapdh_M_at 13.3518
AFFX-Cf_P450-2E1_3_s_at 2.96697

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM520203.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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