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Sample GSM1293449 Query DataSets for GSM1293449
Status Public on Dec 19, 2013
Title HS983a cells at passage 15
Sample type genomic
 
Source name human ES cells line HS983a
Organism Homo sapiens
Characteristics cell line: HS983a
cell type: human ES cells
passage: passage 15
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 HS983a p15
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 -0.137387 1.733138 nan nan
CN_473964 2.000000 1 61796 -0.080440 1.733183 nan nan
CN_473965 2.000000 1 61811 -0.292381 1.733192 nan nan
CN_473981 2.000000 1 62908 -0.055621 1.733863 nan nan
CN_473982 2.000000 1 62925 -0.385616 1.733873 nan nan
CN_497981 2.000000 1 72764 0.086176 1.739908 nan nan
CN_502615 2.000000 1 85924 0.326668 1.748009 nan nan
CN_502613 2.000000 1 85986 -0.919274 1.748047 nan nan
CN_502614 2.000000 1 86312 -0.001295 1.748248 nan nan
CN_502616 2.000000 1 86329 0.262908 1.748258 nan nan
CN_502843 2.000000 1 98590 -0.025453 1.755791 nan nan
CN_466171 2.000000 1 228694 0.055693 1.332488 nan nan
CN_468414 2.000000 1 229063 -0.703443 1.332638 nan nan
CN_468412 2.000000 1 229146 -0.685063 1.332672 nan nan
CN_468413 2.000000 1 229161 -0.588091 1.332678 nan nan
CN_470565 2.000000 1 229607 -0.385910 1.332859 nan nan
CN_468424 2.000000 1 235658 -0.059903 1.335335 nan nan
CN_468425 2.000000 1 235716 0.093855 1.335359 nan nan
CN_460512 2.000000 1 356431 0.946682 5.815234 nan nan
CN_460513 2.000000 1 356530 0.765063 5.815233 nan nan

Total number of rows: 1813281

Table truncated, full table size 114135 Kbytes.




Supplementary file Size Download File type/resource
GSM1293449_983a_p15.CN5.CNCHP.gz 34.9 Mb (ftp)(http) CNCHP
GSM1293449_LA05_983a_p15_GenomeWideSNP_6_.CEL.gz 29.0 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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