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Sample GSM6433366 Query DataSets for GSM6433366
Status Public on Aug 06, 2022
Title 212477
Sample type genomic
 
Source name Merkel cell carcinoma
Organism Homo sapiens
Characteristics condition: carcinoma
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Data processing The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)
 
Submission date Aug 05, 2022
Last update date Aug 06, 2022
Contact name Thibault FABAS
Organization name CHU Nice
Lab Génétiques des Tumeurs Solides
Street address 28 av Valombrose
City NICE
ZIP/Postal code 06107
Country France
 
Platform ID GPL21558
Series (1)
GSE210602 BRCAness and Merkel cell carcinoma: Comprehensive molecular study of 35 cases and meta-analysis of the literature

Supplementary file Size Download File type/resource
GSM6433366_212477-A_OncoScan_CNV_.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM6433366_212477-C_OncoScan_CNV_.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM6433366_212477.OSCHP.gz 15.5 Mb (ftp)(http) OSCHP
GSM6433366_212477.probeset.txt.gz 5.4 Mb (ftp)(http) TXT
Processed data provided as supplementary file

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