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Sample GSM377521 Query DataSets for GSM377521
Status Public on Mar 01, 2010
Title human embryonic stem cell line CCTL-14 p49
Sample type genomic
 
Source name human embryonic stem cell line CCTL-14 p49
Organism Homo sapiens
Characteristics cell type: human embryonic stem cell
cell line: CCTL-14 p49
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 0.001935 AB 2618.708740 2638.119629
SNP_A-1967418 BB 0.001962 BB 341.802063 714.996338
SNP_A-1969580 BB 0.011764 BB 947.794861 3887.762939
SNP_A-4263484 BB 0.001542 BB 390.682281 1434.653076
SNP_A-1978185 AA 0.009055 AA 1048.331665 464.674347
SNP_A-4264431 AA 0.006503 AA 2134.579834 308.431854
SNP_A-1980898 BB 0.003485 BB 297.293060 690.244873
SNP_A-1983139 AA 0.002433 AA 3792.833496 781.180420
SNP_A-4265735 AB 0.005994 AB 1478.399292 1482.736816
SNP_A-1995832 BB 0.005705 BB 597.923096 1938.392700
SNP_A-1995893 BB 0.008305 BB 501.548096 2877.236328
SNP_A-1997689 BB 0.004310 BB 697.883484 3582.396729
SNP_A-1997709 AA 0.006786 AA 1149.176270 293.268402
SNP_A-1997896 AB 0.011179 AB 1122.496948 1297.973145
SNP_A-1997922 AB 0.004472 AB 568.632507 556.904968
SNP_A-2000230 AA 0.005222 AA 1960.087524 1125.335938
SNP_A-2000332 AB 0.002264 AB 2555.842773 2810.335693
SNP_A-2000337 AA 0.002952 AA 1590.678589 381.310059
SNP_A-2000342 AA 0.009223 AA 4102.500000 927.234741
SNP_A-4268173 AA 0.003706 AA 1638.492310 277.246979

Total number of rows: 909622

Table truncated, full table size 46145 Kbytes.




Supplementary file Size Download File type/resource
GSM377521.CEL.gz 27.6 Mb (ftp)(http) CEL
GSM377521.chp.gz 12.9 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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