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Sample GSM377558 Query DataSets for GSM377558
Status Public on Mar 01, 2010
Title Reference HapMap sample NA11832_B08
Sample type genomic
 
Source name Reference HapMap sample NA11832_B08
Organism Homo sapiens
Characteristics cell type: reference HapMap
cell line: NA11832_B08
gender: female
Treatment protocol None
Growth protocol Cell lines were grown according to standard conditions.
Extracted molecule genomic DNA
Extraction protocol cell samples were harvested in each collaborative laboratorion, washed with PBS and sent as a frozen cell pellet to analysis laboratory. Genomic DNA was extracted using QIAamp DNA Mini Kit (Qiagen)
Label TdT
Label protocol accordingly manufactures protocol
 
Hybridization protocol accordingly manufactures protocol
Scan protocol accordingly manufactures protocol
Description Hybridized in Finnish DNA Microarray Centre
Data processing For detecting copy number variation in the samples, we utilized Affymetrix Genotyping Console 3.0.1 and Birdseed v2-algorithm. Samples were normalized against 40 International HapMap samples for copy number variation (CNV), Loss of heterozygosity (LOH) and Single nucleotide polymorphism (SNP).
 
Submission date Mar 04, 2009
Last update date Jan 29, 2010
Contact name Elisa Maarit Närvä
E-mail(s) elisa.narva@btk.fi
Organization name University of Turku
Department Turku Centre for Biotechnology
Lab Riitta Lahesmaa
Street address Tykistönkatu 6
City Turku
ZIP/Postal code 20520
Country Finland
 
Platform ID GPL6801
Series (2)
GSE15096 Affymetrix SNP 6.0 array data for human embryonic stem cell lines
GSE15097 High resolution genome wide DNA analysis on a large panel of Human Embryonic stem cell lines

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 0.004012 AB 2759.138672 2790.580811
SNP_A-1967418 BB 0.002436 BB 291.421204 619.050781
SNP_A-1969580 BB 0.003053 BB 1284.943237 5511.301270
SNP_A-4263484 BB 0.006001 BB 435.277588 1229.147217
SNP_A-1978185 AA 0.008191 AA 1134.885864 480.257080
SNP_A-4264431 AB 0.006330 AB 1076.151611 775.106201
SNP_A-1980898 AB 0.001364 AB 576.724182 497.413300
SNP_A-1983139 AA 0.003831 AA 2649.718018 676.437561
SNP_A-4265735 AA 0.002930 AA 1744.817505 462.338226
SNP_A-1995832 BB 0.004922 BB 497.413300 2455.874268
SNP_A-1995893 BB 0.000402 BB 443.074463 2325.192871
SNP_A-1997689 BB 0.002747 BB 681.352356 3419.749756
SNP_A-1997709 AA 0.005826 AA 1403.986938 342.291962
SNP_A-1997896 AB 0.010004 AB 885.772278 1247.649170
SNP_A-1997922 AB 0.003910 AB 597.857849 653.459717
SNP_A-2000230 AA 0.001530 AA 2176.245605 1267.305054
SNP_A-2000332 AA 0.002005 AA 3390.074463 795.526917
SNP_A-2000337 AA 0.001134 AA 1476.564697 329.854614
SNP_A-2000342 AA 0.003957 AA 3192.038574 653.459717
SNP_A-4268173 AA 0.000670 AA 1536.614502 309.672272

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.




Supplementary file Size Download File type/resource
GSM377558.CEL.gz 27.9 Mb (ftp)(http) CEL
GSM377558.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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