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Sample GSM879208 Query DataSets for GSM879208
Status Public on Dec 06, 2012
Title Osteosarcoma cell line HOS [copy number]
Sample type genomic
 
Source name Osteosarcoma cell line HOS
Organism Homo sapiens
Characteristics cell line: HOS
cell type: Osteosarcoma
sample origin: Not available
gender: female
age (yrs): 13
atcc number: CRL-1543
Biomaterial provider ATCC
Growth protocol The osteosarcoma cells were grown in RPMI1640 (Lonza, Basel, Switzerland) or DMEM (Lonza) supplemented with 10 % foetal calf serum (PAA Laboratories GmbH, Pasching, Austria), GlutaMAX (Invitrogen, California, USA) and penicillin/streptomycin (Lonza), at 37°C with 5 % CO2. All cells were split when reaching 80 % confluency. The osteoblast cells were maintained in medium provided by the manufacturer, split when reaching 80 % confluency, and harvested when enough cells for DNA and RNA isolation were obtained.
Extracted molecule genomic DNA
Extraction protocol DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega, Madison, USA).
Label Biotin
Label protocol Standard Affymetrix label protocol
 
Hybridization protocol Standard Affymetrix hyb protocol
Scan protocol Standard Affymetrix scan protocol
Description Osteosarcoma cell line HOS Affymetrix SNP 6
Data processing Quality control was performed using the Genotyping Console v3.0.1 software (Affymetrix), applying the contrast quality control (CQC) algorithm with a minimal call rate of > 86 %. DNA copy number analysis was performed using the Nexus software (BioDiscovery, California, USA), with the SNPRank segmentation algorithm using default settings (threshold of 0.6 for high copy gain, 0.2 for gain, -0.2 for loss and -1.0 for homozygous loss).
 
Submission date Feb 22, 2012
Last update date Dec 06, 2012
Contact name Leonardo A. Meza-Zepeda
E-mail(s) leonardm@rr-research.no
Organization name The Norwegian Radium Hospital
Department Dept. of Tumor Biology
Street address Ullernchausseen 70
City Oslo
ZIP/Postal code N-0310
Country Norway
 
Platform ID GPL6801
Series (2)
GSE36003 Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma [DNA copy number]
GSE36004 Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma.

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AA 0.042414 AA 3233.133789 565.835388
SNP_A-1967418 AB 0.003639 AB 770.546814 287.190277
SNP_A-1969580 BB 0.003021 BB 1604.012817 7391.073730
SNP_A-4263484 BB 0.015877 BB 575.495422 2011.626709
SNP_A-1978185 AA 0.012316 AA 762.915588 376.523834
SNP_A-4264431 AA 0.004322 AA 1808.462646 315.918915
SNP_A-1980898 BB 0.033640 BB 368.280304 743.502991
SNP_A-1983139 AA 0.005058 AA 4475.449219 723.066772
SNP_A-4265735 AA 0.002379 AA 2782.664795 462.472656
SNP_A-1995832 BB 0.003361 BB 693.082275 2736.928467
SNP_A-1995893 BB 0.003518 BB 542.224304 2943.152344
SNP_A-1997689 BB 0.006647 BB 508.630890 3234.466797
SNP_A-1997709 AA 0.005218 AA 1376.414795 297.616791
SNP_A-1997896 BB 0.003581 BB 506.735138 2062.558105
SNP_A-1997922 AA 0.018211 AA 700.337402 367.944824
SNP_A-2000230 AA 0.006883 AA 3870.454590 820.486511
SNP_A-2000332 AA 0.006627 AA 5967.313477 798.410339
SNP_A-2000337 AA 0.000804 AA 1870.211670 326.804626
SNP_A-2000342 AA 0.002186 AA 4778.386719 944.634216
SNP_A-4268173 AA 0.000277 AA 2170.965576 362.079773

Total number of rows: 909622

Table truncated, full table size 46127 Kbytes.




Supplementary file Size Download File type/resource
GSM879208_HOS.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM879208_HOS.birdseed-v2.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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