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Sample GSM377571 Query DataSets for GSM377571
Status Public on Mar 01, 2010
Title Reference HapMap sample NA12753_A01
Sample type genomic
 
Source name Reference HapMap sample NA12753_A01
Organism Homo sapiens
Characteristics cell type: reference HapMap
cell line: NA12753_A01
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 BB 0.007568 BB 632.688782 4716.492188
SNP_A-1967418 AB 0.004384 AB 533.203125 478.095184
SNP_A-1969580 BB 0.005088 BB 1193.668091 4432.018555
SNP_A-4263484 AB 0.001928 AB 1366.332764 1094.281616
SNP_A-1978185 AA 0.001788 AA 1408.808838 405.158844
SNP_A-4264431 AA 0.005985 AA 1738.631226 291.321991
SNP_A-1980898 AB 0.002902 AB 649.225830 514.389526
SNP_A-1983139 AA 0.009093 AA 3151.250977 915.284851
SNP_A-4265735 BB 0.007242 BB 615.462585 2354.573242
SNP_A-1995832 AB 0.001773 AB 1693.664185 1348.122681
SNP_A-1995893 AB 0.005617 AB 1495.633667 1959.449829
SNP_A-1997689 BB 0.010422 BB 589.432068 3758.844482
SNP_A-1997709 AA 0.008749 AA 2009.869873 281.913116
SNP_A-1997896 AA 0.003646 AA 1182.316162 454.400360
SNP_A-1997922 AB 0.001629 AB 717.020935 635.318481
SNP_A-2000230 AB 0.006858 AB 1401.503418 2336.796143
SNP_A-2000332 AB 0.003589 AB 2330.513916 2540.096680
SNP_A-2000337 AA 0.001015 AA 1515.920532 347.221191
SNP_A-2000342 AA 0.004337 AA 3651.044922 896.972351
SNP_A-4268173 AB 0.003194 AB 807.989014 806.732727

Total number of rows: 909622

Table truncated, full table size 46139 Kbytes.




Supplementary file Size Download File type/resource
GSM377571.CEL.gz 29.3 Mb (ftp)(http) CEL
GSM377571.chp.gz 13.1 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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