NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM377567 Query DataSets for GSM377567
Status Public on Mar 01, 2010
Title Reference HapMap sample NA12740_C6
Sample type genomic
 
Source name Reference HapMap sample NA12740_C6
Organism Homo sapiens
Characteristics cell type: reference HapMap
cell line: NA12740_C6
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 0.003318 BB 683.557861 4488.440918
SNP_A-1967418 BB 0.004089 BB 325.092072 572.779480
SNP_A-1969580 BB 0.006292 BB 919.316284 4827.056152
SNP_A-4263484 BB 0.004173 BB 338.111603 1360.232422
SNP_A-1978185 AA 0.001557 AA 1221.473145 383.446167
SNP_A-4264431 AB 0.012389 AB 1065.079468 710.403137
SNP_A-1980898 AB 0.005670 AB 488.945404 528.238892
SNP_A-1983139 AA 0.002971 AA 2969.009521 603.120667
SNP_A-4265735 AB 0.001663 AB 1203.537231 1378.117798
SNP_A-1995832 BB 0.000603 BB 555.036743 2268.188232
SNP_A-1995893 BB 0.003686 BB 517.182556 2298.948486
SNP_A-1997689 BB 0.005273 BB 522.884399 2619.459717
SNP_A-1997709 AA 0.003023 AA 1338.243164 272.256805
SNP_A-1997896 AA 0.007808 AA 1429.787842 373.247101
SNP_A-1997922 BB 0.000968 BB 393.335205 795.088013
SNP_A-2000230 AA 0.002107 AA 2260.945801 1077.063110
SNP_A-2000332 AB 0.010579 AB 2079.623779 2399.112305
SNP_A-2000337 AA 0.001153 AA 1391.243408 370.099792
SNP_A-2000342 AA 0.005707 AA 2793.170410 653.001160
SNP_A-4268173 AA 0.005833 AA 1620.740479 256.936707

Total number of rows: 909622

Table truncated, full table size 46142 Kbytes.




Supplementary file Size Download File type/resource
GSM377567.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM377567.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap