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Sample GSM1319241 Query DataSets for GSM1319241
Status Public on May 20, 2015
Title SEES1 at passage 4
Sample type genomic
 
Source name human embryonic stem cells
Organism Homo sapiens
Characteristics cell line: SEES1
passage: 4
Growth protocol The SEES lines were routinely cultured onto a feeder layer of freshly plated gamma-irradiated MEFs in the human ES cell culture media. The media consisted of KnockoutTM-Dulbecco’s modified Eagle’s medium supplemented with 20% KnockoutTM-Serum Replacement, 2 mM Glutamax-I, 0.1 mM non-essential amino acids, 50 U/ml penicillin-50 μg/ml streptomycin (Pen-Strep), 0.055 mM beta-mercaptoethanol, and recombinant human full-length bFGF.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA extracted from cells using QIAamp DNA Mini Kit (Qiagen).
Label C-Bio and A-DNP
Label protocol Illumina's standard protocol
 
Hybridization protocol DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.
Scan protocol The BeadChip array was scanned using the iScan (Illumina)
Description Genomic DNA extracted from cells was genotyped using HumanCytoSNP-12 v2.1 DNA Analysis BeadChip Kit (Illumina).
Data processing Data were processed using GenomeStudio V2011.1
 
Submission date Jan 30, 2014
Last update date May 20, 2015
Contact name Akihiro Umezawa
E-mail(s) umezawa@1985.jukuin.keio.ac.jp
Phone 81-3-5494-7047
Organization name National Center for Child Health and Development
Department Center for Regenerative Medicine
Street address 2-10-1 Okura
City Setagaya-ku
State/province Tokyo
ZIP/Postal code 157-8535
Country Japan
 
Platform ID GPL13829
Series (1)
GSE54576 An analysis of genomic structural alteration in three human ES cell lines.

Data table header descriptions
ID_REF
VALUE Genotype: AA,AB,BB,or NC (no call)
GC_SCORE
Theta
R
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE GC_SCORE Theta R B_Allele_Freq Log_R_Ratio
cnvi0111185 NC 0 0.9697456 1.517113 0.9925992 0.2445089
cnvi0111186 NC 0 0.03734855 0.5913723 0.01057599 0.1950302
cnvi0111187 NC 0 0.9759264 1.604535 0.9910137 0.09831454
cnvi0111188 NC 0 0.007774306 1.341662 0 0.02176281
cnvi0111189 NC 0 0.02908281 1.460314 0.006746962 -0.01436276
cnvi0111190 NC 0 0.01400201 0.4941236 0 0.1677895
cnvi0111191 NC 0 0.03907158 1.082866 0.002810303 0.250094
cnvi0111192 NC 0 0.02534627 1.020611 0.00413306 -0.1665369
cnvi0111193 NC 0 0.009559468 1.390772 0 0.266769
cnvi0111194 NC 0 0.9890342 1.234335 1 -0.02426895
cnvi0111195 NC 0 0.05220079 2.144612 0.02384632 0.001562991
cnvi0111196 NC 0 0.9948236 1.12097 1 -0.1410493
cnvi0111197 NC 0 0.045529 0.8543873 0.02859952 0.001013138
cnvi0111198 NC 0 0.973016 1.341123 1 -0.003657285
cnvi0111199 NC 0 0.02581748 1.356501 0.01505637 -0.02212958
cnvi0111200 NC 0 0.9822412 0.8313904 0.9951191 -0.009937423
cnvi0111201 NC 0 0.03328504 1.065826 0.004610999 0.2836655
cnvi0111202 NC 0 0.9265649 1.329521 0.9806646 -0.01389705
cnvi0111203 NC 0 0.07324065 1.927533 0.03371413 0.06101992
cnvi0111204 NC 0 0.9892448 1.450512 1 0.3361134

Total number of rows: 298563

Table truncated, full table size 17859 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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