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Sample GSM629054 Query DataSets for GSM629054
Status Public on Dec 10, 2011
Title Blood-H1
Sample type RNA
 
Source name peripheral blood
Organism Canis lupus familiaris
Characteristics disease state: normal
Extracted molecule total RNA
Extraction protocol Peripheral blood samples were collected in EDTA containing tubes and diluted 1:6 in Erythrocyte lysis buffer (0.13 M NH4CL, 0.1 M KHC03 and 1.2x10-4 M EDTA ) in order to eliminate red blood cells. After incubation for 30 minutes at 4ºC samples were centrifuged at 1500 rpm for 15 minutes and the supernatant was discharged in order to obtain a pellet composed mainly by peripheral blood leukocytes (PBL). The procedure was repeated until a clear, white pellet was obtained. The two canine mammary carcinoma cell lines, CMM115 and CMM26, were cultivated in RPMI1640 medium supplemented with 10% bovine fetal serum. The cells were incubated in 75 cm3 tissue culture flasks, with air containing 5 % CO2 at 37oC. After the formation of a confluent monolayer, cells were harvested by washing once with PBS, pH 7,3 and incubation with in PBS containing 0,02 % EDTA and 0,25 % trypsin for five minutes a 37°C. RNA isolation from the PBL pellets and cell lines was performed using a commercial kit (Nucleo Spin RNAII, Macherey-Nagel) according to the manufacturer’s instructions with subsequent DNAse treatment.
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
Data processing Affymetrix CEL files were imported into Partek Genomic Suite Software (Version 6.5, Partek Inc., St. Louis, USA) and processed by the implemented RMA workflow (median polish probe set summarization, RMA background correction, quantile normalization).
 
Submission date Nov 23, 2010
Last update date Dec 10, 2011
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)
GSE25586 Identification of Six Potential Markers for the Detection of Circulating Canine Mammary Tumor Cells in the Peripheral Blood

Data table header descriptions
ID_REF
VALUE normalized log2 signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 8.43926
AFFX-BioB-5_at 8.62017
AFFX-BioB-M_at 8.86475
AFFX-BioC-3_at 10.5068
AFFX-BioC-5_at 9.83671
AFFX-BioDn-3_at 12.1108
AFFX-BioDn-5_at 10.7163
AFFX-Cf_Actin_3_at 12.85
AFFX-Cf_Actin_5_s_at 12.2944
AFFX-Cf_Actin_M_at 11.4682
AFFX-Cf_AdrenRecpt_3_at 6.98155
AFFX-Cf_AdrenRecpt_5_at 5.59786
AFFX-Cf_AdrenRecpt_M_at 5.46665
AFFX-Cf_G-6-PDH_3_at 3.7805
AFFX-Cf_G-6-PDH_5_at 4.59007
AFFX-Cf_G-6-PDH_M_at 3.73996
AFFX-Cf_Gapdh_3_at 13.6266
AFFX-Cf_Gapdh_5_at 13.5492
AFFX-Cf_Gapdh_M_at 13.4113
AFFX-Cf_P450-2E1_3_s_at 2.94254

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM629054.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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