NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM629058 Query DataSets for GSM629058
Status Public on Dec 10, 2011
Title CMM26
Sample type RNA
 
Source name mammary carcinoma cell line
Organism Canis lupus familiaris
Characteristics cell line: CMM26
disease state: tumor
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 6.96873
AFFX-BioB-5_at 7.26854
AFFX-BioB-M_at 7.32758
AFFX-BioC-3_at 8.90745
AFFX-BioC-5_at 8.26375
AFFX-BioDn-3_at 11.0123
AFFX-BioDn-5_at 9.40169
AFFX-Cf_Actin_3_at 13.1731
AFFX-Cf_Actin_5_s_at 12.7461
AFFX-Cf_Actin_M_at 12.0885
AFFX-Cf_AdrenRecpt_3_at 6.97528
AFFX-Cf_AdrenRecpt_5_at 5.71071
AFFX-Cf_AdrenRecpt_M_at 5.41257
AFFX-Cf_G-6-PDH_3_at 3.8057
AFFX-Cf_G-6-PDH_5_at 4.74725
AFFX-Cf_G-6-PDH_M_at 3.48076
AFFX-Cf_Gapdh_3_at 13.1861
AFFX-Cf_Gapdh_5_at 12.9807
AFFX-Cf_Gapdh_M_at 12.8984
AFFX-Cf_P450-2E1_3_s_at 2.91071

Total number of rows: 43035

Table truncated, full table size 1188 Kbytes.




Supplementary file Size Download File type/resource
GSM629058.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap