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Sample GSM1014057 Query DataSets for GSM1014057
Status Public on Jun 12, 2015
Title Embryonal rhabdomyosarcoma in a Costello syndrome patient
Sample type genomic
Source name Embryonal rhabdomyosarcoma in a Costello syndrome patient
Organism Homo sapiens
Characteristics tissue: tumor
disease state: Embryonal rhabdomyosarcoma in a Costello syndrome patient
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from a fresh-frozen tumor sample using the Quiagen Gentra Puregene Kit, as recommended by the Affymetrix CytoScan Assay user manual. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.
Label biotin
Label protocol As per manufacturer (Affymetrix)
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to the array (Affymetrix GeneChip Hybridization Oven 645) according to the manufacturer's instructions.
Scan protocol The array was then washed using Affymetrix GeneChip fluidics station 450, and scanned using the Affymetrix GeneChip Scanner 3000.
Data processing The array image was acquired using Affymetrix GeneChip Command Console Software. For confirmation, two Cytoscan HD arrays were performed for the tumor which gave similar results. Their raw DAT files were aligned and averaged by a proprietary C++ program (Microsoft, USA) for further analysis. CEL and CYCHP files were generated from the averaged DAT file using Chromosome Analysis Suite 1.2.2 from Affymetrix.
Allele peak data and SNP copy numbers were analyzed. The standard bi-allelic genotype calls (AA, AB, BB) do not apply in the tumor's trisomies. The quality metric "MAPD < 25" was fulfilled. According to the manufacturer the quality metrics "SNPQC" and "Waviness SD" do not apply in this solid tumor (
Submission date Oct 02, 2012
Last update date Jun 12, 2015
Contact name Jan Menke
Organization name University Hospital Goettingen
Street address Robert-Koch-Strasse 40
City Goettingen
ZIP/Postal code 37075
Country Germany
Platform ID GPL16131
Series (1)
GSE41297 SNP array data for embryonal rhabdomyosarcoma in a patient with Costello syndrome

Data table header descriptions

Data table
C-7SARK -0.116607 0.082821 2.316859
C-4WYLN 0.281072 0.158405 2.315115
C-3BFNY 0.021391 -0.035566 2.312954
C-7ONNE 0.059661 0.039860 2.312760
C-6HYCN 0.186477 0.007162 2.312858
C-7SCGC 0.013743 0.082210 2.311980
C-7RZQQ -0.021510 -0.108668 2.311344
C-7RZWZ -0.232345 -0.034339 2.310076
C-7SEBI 0.160624 0.110868 2.309832
C-7RZIL 0.037259 0.183974 2.311439
C-4NQTX 0.042143 0.002735 2.312818
C-7SDKW 0.131477 0.073928 2.312471
S-3WRNV null null null
C-7RXVK 0.365897 0.193779 2.313069
C-4LHKS 0.430562 0.262180 2.313905
C-7RWHE -0.281008 0.101089 2.314893
C-7SBEJ 0.207248 0.165661 2.316034
C-7RYJO -0.003586 0.275477 2.317892
C-7SEGS 0.411702 0.335071 2.318722
C-4LLXK 0.289430 0.205799 2.320538

Total number of rows: 2749693

Table truncated, full table size 95136 Kbytes.

Supplementary file Size Download File type/resource
GSM1014057_237be5d4-4845-4162.CEL.gz 29.7 Mb (ftp)(http) CEL
GSM1014057_237be5d4-4845-4162.cyhd.cychp.gz 79.9 Mb (ftp)(http) CYCHP
Processed data included within Sample table
Processed data provided as supplementary file

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