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Sample GSM377522 Query DataSets for GSM377522
Status Public on Mar 01, 2010
Title human embryonic stem cell line CCTL-14 p38
Sample type genomic
 
Source name human embryonic stem cell line CCTL-14 p38
Organism Homo sapiens
Characteristics cell type: human embryonic stem cell
cell line: CCTL-14 p38
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 0.002386 AB 2444.201660 2283.366699
SNP_A-1967418 BB 0.003640 BB 354.115509 746.168152
SNP_A-1969580 BB 0.002176 BB 1082.699219 5061.126465
SNP_A-4263484 BB 0.014385 BB 482.144684 1856.289185
SNP_A-1978185 AA 0.007767 AA 1664.149048 375.231873
SNP_A-4264431 AA 0.004861 AA 2203.166016 329.005981
SNP_A-1980898 BB 0.011042 BB 386.883301 724.231262
SNP_A-1983139 AA 0.004231 AA 3926.239014 860.333191
SNP_A-4265735 AB 0.005633 AB 1167.799927 1116.213623
SNP_A-1995832 BB 0.011672 BB 512.061035 1613.781128
SNP_A-1995893 BB 0.004295 BB 476.244446 2700.809570
SNP_A-1997689 BB 0.003959 BB 677.505493 3070.352783
SNP_A-1997709 AA 0.006363 AA 1168.217285 294.349396
SNP_A-1997896 AB 0.008110 AB 1049.744141 1308.178223
SNP_A-1997922 AB 0.005514 AB 541.824280 588.225830
SNP_A-2000230 AA 0.006582 AA 2687.431396 1195.920044
SNP_A-2000332 AB 0.006474 AB 2913.297119 2750.480713
SNP_A-2000337 AA 0.003059 AA 1519.544556 301.764923
SNP_A-2000342 AA 0.000812 AA 3461.506348 796.488098
SNP_A-4268173 AA 0.002298 AA 1564.280029 329.256683

Total number of rows: 909622

Table truncated, full table size 46151 Kbytes.




Supplementary file Size Download File type/resource
GSM377522.CEL.gz 28.6 Mb (ftp)(http) CEL
GSM377522.chp.gz 13.0 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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