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Sample GSM377516 Query DataSets for GSM377516
Status Public on Mar 01, 2010
Title human embryonic stem cell line H7 s6 teratoma p127
Sample type genomic
 
Source name human embryonic stem cell line H7 s6 teratoma p127
Organism Homo sapiens
Characteristics cell type: human embryonic stem cell
cell line: H7 s6 teratoma p127
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 0.004280 BB 555.260193 3954.387695
SNP_A-1967418 AA 0.011963 AA 908.888794 612.375610
SNP_A-1969580 BB 0.009865 BB 1050.614136 5681.662598
SNP_A-4263484 AB 0.024494 AB 1629.787598 1452.399292
SNP_A-1978185 AA 0.017635 AA 1751.829956 264.046936
SNP_A-4264431 AA 0.052106 AA 2982.883789 291.150635
SNP_A-1980898 BB 0.019419 BB 298.563660 1204.077881
SNP_A-1983139 AA 0.015746 AA 4871.160156 822.744812
SNP_A-4265735 AA 0.081299 AA 3919.100586 432.735779
SNP_A-1995832 AA 0.008862 AA 2162.705078 1014.786926
SNP_A-1995893 AA 0.007464 AA 2802.180664 2077.654297
SNP_A-1997689 BB 0.011083 BB 512.693665 3537.555908
SNP_A-1997709 AA 0.018173 AA 2022.925171 234.941284
SNP_A-1997896 AB 0.012753 AB 1356.351685 1602.526245
SNP_A-1997922 AA 0.002870 AA 880.391846 315.556854
SNP_A-2000230 AA 0.015090 AA 2279.274902 1868.662720
SNP_A-2000332 AA 0.031403 AA 4238.134277 2754.309814
SNP_A-2000337 AA 0.025881 AA 2044.556885 394.713226
SNP_A-2000342 AA 0.029831 AA 4764.488770 696.918030
SNP_A-4268173 AB 0.038064 AB 1870.263550 749.125244

Total number of rows: 909622

Table truncated, full table size 46144 Kbytes.




Supplementary file Size Download File type/resource
GSM377516.CEL.gz 23.6 Mb (ftp)(http) CEL
GSM377516.chp.gz 12.6 Mb (ftp)(http) CHP
Processed data provided as supplementary file

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