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Sample GSM879206 Query DataSets for GSM879206
Status Public on Dec 06, 2012
Title Osteosarcoma cell line 143B [copy number]
Sample type genomic
 
Source name Osteosarcoma cell line 143B
Organism Homo sapiens
Characteristics cell line: 143B
cell type: Osteosarcoma
sample origin: Not available
gender: female
age (yrs): 13
atcc number: CRL-8303
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 143B 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 AB 0.004303 AB 2846.972656 2274.051758
SNP_A-1967418 AB 0.003683 AB 899.991516 658.548706
SNP_A-1969580 BB 0.009280 BB 1685.410522 8860.123047
SNP_A-4263484 BB 0.003277 BB 434.866791 2460.728027
SNP_A-1978185 AA 0.004257 AA 1019.308533 371.230103
SNP_A-4264431 AA 0.006236 AA 2914.376465 375.447205
SNP_A-1980898 BB 0.006605 BB 406.721527 1060.857788
SNP_A-1983139 AA 0.003213 AA 5415.908203 994.160034
SNP_A-4265735 AA 0.002503 AA 3214.804199 491.172638
SNP_A-1995832 BB 0.002582 BB 566.018799 2850.162842
SNP_A-1995893 BB 0.001226 BB 515.735535 3524.449219
SNP_A-1997689 BB 0.001325 BB 702.249512 4754.066406
SNP_A-1997709 AA 0.004257 AA 1618.659302 300.799713
SNP_A-1997896 AB 0.012728 AB 1003.315735 2297.392334
SNP_A-1997922 AB 0.006767 AB 829.072937 536.225952
SNP_A-2000230 AA 0.012881 AA 4682.646484 972.046265
SNP_A-2000332 AA 0.028400 AA 7305.076172 911.967590
SNP_A-2000337 AA 0.002035 AA 2310.585449 376.195068
SNP_A-2000342 AA 0.013683 AA 5579.977539 760.274902
SNP_A-4268173 AB 0.008979 AB 2508.602783 1396.492432

Total number of rows: 909622

Table truncated, full table size 46138 Kbytes.




Supplementary file Size Download File type/resource
GSM879206_143B.CEL.gz 27.0 Mb (ftp)(http) CEL
GSM879206_143B.birdseed-v2.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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