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Sample GSM1293451 Query DataSets for GSM1293451
Status Public on Dec 19, 2013
Title control H1 cells at passage 56
Sample type genomic
 
Source name human ES cells line H1
Organism Homo sapiens
Characteristics cell line: H1 (control)
cell type: human ES cells
passage: passage 56
Growth protocol Human Es cells were grown on laminin-521
Extracted molecule genomic DNA
Extraction protocol DNA was extracted using Qiagen DNA Mini Kit
Label Biotin
Label protocol According to Affymetrics instructions
 
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/G
Description H1 p56
Data processing The array image was acquired using Affymetrix GeneChip®Command Console 3.1. The CEL files were analyzed using Affymetrix Genotyping Console version 4.1.4.840. Copy Number/LOH analysis was performed according to the Genotyping Console manual, using a set of 75 healthy individuals as a reference (75_samples_ref.REF).
CNCHP files containing information on the observed copy number of genomic segments. One REF file produced by the Batch Sample Mode of copy number analysis in the Affymetrix Genotyping Console.
 
Submission date Dec 18, 2013
Last update date Dec 19, 2013
Contact name Sergey Rodin
Organization name Karolinska institute
Street address Scheelesvag 2, Plan 4:B1
City Stockholm
ZIP/Postal code 17177
Country Sweden
 
Platform ID GPL6801
Series (1)
GSE53436 Affymetrix SNP array data for various human ES cell lines

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 61723 0.185906 2.181500 nan nan
CN_473964 2.000000 1 61796 0.009894 2.181563 nan nan
CN_473965 2.000000 1 61811 0.082415 2.181576 nan nan
CN_473981 2.000000 1 62908 -0.358906 2.182518 nan nan
CN_473982 2.000000 1 62925 0.079162 2.182532 nan nan
CN_497981 2.000000 1 72764 0.160892 2.191082 nan nan
CN_502615 2.000000 1 85924 0.015352 2.202767 nan nan
CN_502613 2.000000 1 85986 -0.132429 2.202822 nan nan
CN_502614 2.000000 1 86312 0.305658 2.203115 nan nan
CN_502616 2.000000 1 86329 0.280976 2.203130 nan nan
CN_502843 2.000000 1 98590 0.190721 2.214217 nan nan
CN_466171 2.000000 1 228694 -0.056692 1.372771 nan nan
CN_468414 2.000000 1 229063 -0.713927 1.372762 nan nan
CN_468412 2.000000 1 229146 -0.414943 1.372760 nan nan
CN_468413 2.000000 1 229161 0.227796 1.372760 nan nan
CN_470565 2.000000 1 229607 -0.542463 1.372749 nan nan
CN_468424 2.000000 1 235658 -0.160756 1.372605 nan nan
CN_468425 2.000000 1 235716 -0.451474 1.372603 nan nan
CN_460512 2.000000 1 356431 0.264010 3.043319 nan nan
CN_460513 2.000000 1 356530 0.409250 3.043319 nan nan

Total number of rows: 1813281

Table truncated, full table size 114269 Kbytes.




Supplementary file Size Download File type/resource
GSM1293451_H1.CN5.CNCHP.gz 34.8 Mb (ftp)(http) CNCHP
GSM1293451_VT03_H1.CEL.gz 30.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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