NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM768927 Query DataSets for GSM768927
Status Public on Sep 01, 2011
Title Fibroblast-B
Sample type genomic
 
Source name Dermal fibroblast derived from patient B
Organism Homo sapiens
Characteristics cell type: Dermal fibroblast
genetic modification: None
Treatment protocol n/a
Growth protocol Cell lines were grown according to standard conditions, and as described in associated manuscript
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using DNeasy kit (Qiagen) according to the manufacturer's instruction.
Label C-Bio and A-DNP
Label protocol As per standard Illumina protocol.
 
Hybridization protocol DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.
Scan protocol The BeadChip arrays were scanned using the iScan (Illumina)
Description Genomic DNA extracted from fibroblasts was genotyped using Illumina CytoSNP12 v2.1 BeadChips.
Data processing The scanned data files were processed by GenomeStudio GT module (Illumina). GenomeStudio was also used to call genotype and calculate LogR ratio and B allele frequency using a cluster file (HumanCytoSNP-12v2-1_A.egt) supplied by Illumina.
 
Submission date Jul 29, 2011
Last update date Sep 01, 2011
Contact name Kosuke Yusa
Organization name Wellcome Trust Sanger Institute
Street address Wellcome Trust Genome Campus
City Hinxton
State/province Cambridgeshire
ZIP/Postal code CB10 1SA
Country United Kingdom
 
Platform ID GPL13829
Series (1)
GSE31035 SNP analysis of human induced pluripotent stem cells

Data table header descriptions
ID_REF
VALUE AB-type genotype call
Genotype_call
B_Allele_Freq
Log_R_Ratio

Data table
ID_REF VALUE Genotype_call B_Allele_Freq Log_R_Ratio
cnvi0111185 NC 0.9993 -0.1733
cnvi0111186 NC 0 0.2509
cnvi0111187 NC 0.9997 0.26
cnvi0111188 NC 0 0.1612
cnvi0111189 NC 0.0096 0.1144
cnvi0111190 NC 0 0.3659
cnvi0111191 NC 0.0056 -0.0672
cnvi0111192 NC 0 0.2461
cnvi0111193 NC 0 -0.0726
cnvi0111194 NC 0.9894 -0.2658
cnvi0111195 NC 0.008 0.155
cnvi0111196 NC 0.9997 -0.0736
cnvi0111197 NC 0 0.0646
cnvi0111198 NC 0.991 0.1139
cnvi0111199 NC 0.01 -0.1978
cnvi0111200 NC 0.9932 -0.0468
cnvi0111201 NC 0.0013 -0.0401
cnvi0111202 NC 0.9925 0.0847
cnvi0111203 NC 0.0221 0.2038
cnvi0111204 NC 0.9983 0.1184

Total number of rows: 299140

Table truncated, full table size 8524 Kbytes.




Supplementary file Size Download File type/resource
GSM768927_sample1-matrixsignal.txt.gz 3.5 Mb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap