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Sample GSM1566878 Query DataSets for GSM1566878
Status Public on Dec 17, 2014
Title stem cell line BG03C
Sample type genomic
 
Source name stem cell line BG03C
Organism Homo sapiens
Characteristics cell type: embryonic stem cell
cell line: BG03
Treatment protocol None
Growth protocol Cells were grown on MEF feeders in standard conditions and separated using collagenase.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from embryonic stem cells using Qiagen Dneasy Tissue kit. DNA quality and quantity was assessed using a Tecan plate reader, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to Genome-Wide Human SNP Array 6.0
Data processing The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 4.0). Copy number values for individual SNPs were determined by Affymetrix Genotyping Console Software v.4.0.
chromosome, chromosome region start, chromosome region end, region=copy number region, signal=signal intensity, call=copy number state, confidence
 
Submission date Dec 16, 2014
Last update date Dec 17, 2014
Contact name William Freed
Organization name NIDA NIH
Street address 333 CASSELL DRIVE
City BALTIMORE
State/province MD
ZIP/Postal code 21224
Country USA
 
Platform ID GPL6801
Series (1)
GSE64241 Affymetrix SNP copy number data for embryonic stem cell samples

Data table header descriptions
ID_REF
VALUE CN STATE
CHROMOSOME
POSITION
LOG2 RATIO
SMOOTH SIGNAL
LOH
ALLELE DIFFERENCE

Data table
ID_REF VALUE CHROMOSOME POSITION LOG2 RATIO SMOOTH SIGNAL LOH ALLELE DIFFERENCE
CN_473963 2.000000 1 51586 0.035410 2.268036 nan nan
CN_473964 2.000000 1 51659 -0.111808 2.268103 nan nan
CN_473965 2.000000 1 51674 -0.049498 2.268116 nan nan
CN_473981 2.000000 1 52771 0.373775 2.269115 nan nan
CN_473982 2.000000 1 52788 -0.107384 2.269130 nan nan
CN_497981 2.000000 1 62627 0.010634 2.277945 nan nan
CN_502615 2.000000 1 75787 0.194011 2.289240 nan nan
CN_502613 2.000000 1 75849 0.148170 2.289292 nan nan
CN_502614 2.000000 1 76175 0.127329 2.289563 nan nan
CN_502616 2.000000 1 76192 0.613789 2.289577 nan nan
CN_502843 2.000000 1 88453 -0.097339 2.299415 nan nan
CN_466171 2.000000 1 218557 0.196111 2.381252 nan nan
CN_468414 2.000000 1 218926 0.003185 2.381285 nan nan
CN_468412 2.000000 1 219009 -0.041029 2.381293 nan nan
CN_468413 2.000000 1 219024 0.131724 2.381294 nan nan
CN_470565 2.000000 1 219470 0.338531 2.381335 nan nan
CN_468424 2.000000 1 225521 0.285073 2.381888 nan nan
CN_468425 2.000000 1 225579 0.066485 2.381894 nan nan
CN_460512 2.000000 1 346294 0.569548 2.968995 nan nan
CN_460513 2.000000 1 346393 0.064058 2.968993 nan nan

Total number of rows: 1813441

Table truncated, full table size 114244 Kbytes.




Supplementary file Size Download File type/resource
GSM1566878_BG03C.CEL.gz 33.7 Mb (ftp)(http) CEL
GSM1566878_BG03C.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
GSM1566878_BG03C.cnvchp.gz 12.2 Kb (ftp)(http) CNVCHP
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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