NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1942545 Query DataSets for GSM1942545
Status Public on May 01, 2016
Title Skin_Fibroblast_c122
Sample type genomic
 
Source name Skin biopsy, fibroblast, cell 122
Organism Homo sapiens
Characteristics gender: Female
tissue: skin fibroblast
Treatment protocol Following overnight treatment of the biopt with 400U/ml collagenase in culture medium, single cells were washed in 1xPBS (Thermo Scientific, USA).
Growth protocol Single fibroblasts were isolated from a fresh skin biopsy.
Extracted molecule genomic DNA
Extraction protocol The genome of collected single cells was amplified using GenomiphiV2 (GE Healthcare).
Label Cy5,Cy3
Label protocol The samples were not labelled before the hybridization. The staining is based on post-hybridization Cy5/Cy3 staining by extension, according to the manual of Infinium II Assay (Illumina, USA).
 
Hybridization protocol According to the manual of Infinium II Assay (Illumina, USA)
Scan protocol According to the manual of Infinium II Assay (Illumina, USA)
Description Genomiphi V2 whole genome amplified material.
Data processing Raw data were further processed using GenomeStudio.
 
Submission date Nov 17, 2015
Last update date May 01, 2016
Contact name Eftychia Dimitriadou
E-mail(s) eftychia.dimitriadou@med.kuleuven.be
Organization name KU Leuven
Lab Cytogenetics and Genome Research
Street address Herestraat 49, ON1, bus 602
City Leuven
ZIP/Postal code 3000
Country Belgium
 
Platform ID GPL13829
Series (2)
GSE75093 Segmental chromosomal imbalances arise at high frequency in human fibroblasts (SB_sc_1)
GSE75116 Segmental chromosomal imbalances arise at high frequency in human fibroblasts

Data table header descriptions
ID_REF
VALUE All values were exported from the Genotyping module of GenomeStudio software using an optimal threshold of 0,75.
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
rs10059646 BB 0.8365396 0.9714772 2.327033 0.9911466 0.6836234
rs10074911 NC 0 0.1703129 2.64196 0.2780064 0.1476059
rs10084637 NC 0.6409326 0.04067083 1.305089 0.001623771 0.5161917
rs1009128 NC 0 0.9824944 0.9117886 0.996752 -0.2140225
rs10111087 BB 0.8685128 0.9866992 1.77678 0.9909226 0.4184707
rs10166589 NC 0.7030756 0.9815203 1.888678 0.9938152 0.354033
rs10166677 NC 0.2328149 0.7206721 0.05713093 0.5819802 -2.42885
rs10200219 NC 0.2767292 0.9821459 1.081369 1 0.01478466
rs10221474 NC 0.665179 0.07957934 0.4072827 0.01464342 -0.5968707
rs10224134 NC 0.254371 0.09537569 0.211443 0.0532083 -2.21906
rs10232915 NC 0.4625357 0.9881902 1.789225 1 0.5505837
rs10239194 NC 0 0.04995519 0.505075 0.07756485 -1.399096
rs10283502 NC 0 0.08357476 2.185014 0 0.5732051
rs10414884 AA 0.8318321 0.0270141 0.7840726 0.001328252 -0.5231707
rs10458479 NC 0 0.9614278 2.026937 0.9668381 0.4634233
rs10468635 NC 0.3845799 0.04036833 0.7495617 0.006130383 -0.06367092
rs10502267 BB 0.8258053 0.9657405 1.989044 0.9922374 0.5745954
rs1065426 NC 0 0.9004813 0.2172114 0.9081874 -2.718147
rs10737933 NC 0.4465662 0.5399489 1.259394 0.4955183 -0.1615662
rs10794411 AA 0.9115698 0.0227507 0.9149218 0 1.164387

Total number of rows: 298563

Table truncated, full table size 17588 Kbytes.




Supplementary file Size Download File type/resource
GSM1942545_9422485012_R03C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942545_9422485012_R03C02_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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