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Sample GSM377577 Query DataSets for GSM377577
Status Public on Mar 01, 2010
Title Reference HapMap sample NA12812_C10
Sample type genomic
 
Source name Reference HapMap sample NA12812_C10
Organism Homo sapiens
Characteristics cell type: reference HapMap
cell line: NA12812_C10
gender: male
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 0.003641 AB 2223.333984 2150.141113
SNP_A-1967418 AB 0.005222 AB 521.933289 493.845306
SNP_A-1969580 BB 0.004107 BB 1366.376587 4989.799316
SNP_A-4263484 BB 0.000733 BB 419.463989 1412.047607
SNP_A-1978185 AA 0.003612 AA 1303.700317 447.434113
SNP_A-4264431 AA 0.006637 AA 1569.205200 294.271912
SNP_A-1980898 BB 0.004994 BB 254.039200 724.804626
SNP_A-1983139 AA 0.008890 AA 2172.223145 539.485962
SNP_A-4265735 AB 0.005638 AB 1106.771240 1133.336060
SNP_A-1995832 AB 0.004323 AB 1942.703247 1694.186523
SNP_A-1995893 AB 0.013994 AB 2060.687012 1814.684448
SNP_A-1997689 BB 0.010756 BB 451.458801 3237.191406
SNP_A-1997709 AA 0.007413 AA 1952.536743 279.670563
SNP_A-1997896 AA 0.003556 AA 1227.048706 426.581390
SNP_A-1997922 AB 0.023504 AB 651.479980 780.503601
SNP_A-2000230 AA 0.000432 AA 2269.025879 1266.187500
SNP_A-2000332 AA 0.004960 AA 3094.095947 882.264282
SNP_A-2000337 AA 0.002555 AA 1331.343750 383.772614
SNP_A-2000342 AA 0.002737 AA 2947.352783 735.295166
SNP_A-4268173 AA 0.003578 AA 1297.564331 291.302765

Total number of rows: 909622

Table truncated, full table size 46143 Kbytes.




Supplementary file Size Download File type/resource
GSM377577.CEL.gz 27.7 Mb (ftp)(http) CEL
GSM377577.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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