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Sample GSM608319 Query DataSets for GSM608319
Status Public on Dec 20, 2010
Title gDNA, Cell Line 4, Sample 1
Sample type genomic
 
Source name Lymphocyte Cell Line
Organism Homo sapiens
Characteristics cell type: Lymphocyte Cell Line
cell line karyotype: 47,XXX
sample type: gDNA
Growth protocol Four human fibroblast cell lines were cultured as suggested by Coriell Cell Repository
Extracted molecule genomic DNA
Extraction protocol Single fibroblast cells underwent alkaline lysis for genomic DNA extraction as described previously (Cui et al., 1989; PNAS 86, 9389-93).
Label biotin
Label protocol Fragmented DNA was biotinylated using the manufacturers recommendations (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930)
 
Hybridization protocol DNA was digested with the NspI restriction enzyme, ligated to an adapter molecule, PCR amplified, fragmented with DNase I, labeled and hybridized to each array according to the manufacturer's instructions (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).
Scan protocol Each array was washed using Affymetrix fluidics station 640, and scanned using the Gene Chip Scanner 7G as recommended (Affymetrix Inc., GeneChip Mapping 500K Assay Manual # 701930).
Description Hybridized to 250K_Nsp
Data processing CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls. Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual) analysis against a reference set of 30 normal females from the HapMap database (www.hapmap.org).
Copy number data not provided by submitter.
 
Submission date Oct 14, 2010
Last update date Dec 20, 2010
Contact name Nathan Treff
Organization name RMA of New Jersey
Street address 111 Madison Ave
City Morristown
ZIP/Postal code 07960
Country USA
 
Platform ID GPL3718
Series (1)
GSE24690 Single Cell Whole Genome Amplification Technique Impacts the Accuracy of SNP Microarray Based Genotyping and Copy Number Analyses

Data table header descriptions
ID_REF
VALUE Genotypes: AA, AB, BB, No Call
CONFIDENCE
RAS1 Relative allele signal for the data in the first probe group
RAS2 Relative allele signal for the data in the second probe group
P-VALUE AA
P-VALUE AB
P-VALUE BB
P-VALUE NO CALL

Data table
ID_REF VALUE CONFIDENCE RAS1 RAS2 P-VALUE AA P-VALUE AB P-VALUE BB P-VALUE NO CALL
AFFX-5Q-123 No Call 0 0 0 0 0 0 0
AFFX-5Q-456 No Call 0 0 0 0 0 0 0
AFFX-5Q-789 No Call 0 0 0 0 0 0 0
AFFX-5Q-ABC No Call 0 0 0 0 0 0 0
AFFX-barcodeA No Call 0 0 0 0 0 0 0
AFFX-barcodeB No Call 0 0 0 0 0 0 0
AFFX-barcodeC No Call 0 0 0 0 0 0 0
AFFX-barcodeD No Call 0 0 0 0 0 0 0
AFFX-barcodeE No Call 0 0 0 0 0 0 0
AFFX-barcodeF No Call 0 0 0 0 0 0 0
AFFX-barcodeG No Call 0 0 0 0 0 0 0
AFFX-barcodeH No Call 0 0 0 0 0 0 0
AFFX-barcodeI No Call 0 0 0 0 0 0 0
AFFX-barcodeJ No Call 0 0 0 0 0 0 0
AFFX-barcodeK No Call 0 0 0 0 0 0 0
AFFX-barcodeL No Call 0 0 0 0 0 0 0
AFFX-barcodeM No Call 0 0 0 0 0 0 0
AFFX-barcodeN No Call 0 0 0 0 0 0 0
AFFX-barcodeO No Call 0 0 0 0 0 0 0
AFFX-barcodeP No Call 0 0 0 0 0 0 0

Total number of rows: 262338

Table truncated, full table size 20526 Kbytes.




Supplementary file Size Download File type/resource
GSM608319.CEL.gz 26.0 Mb (ftp)(http) CEL
GSM608319_gDNA_Cell4_1.CHP.gz 539.0 Kb (ftp)(http) CHP
Processed data not provided for this record
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