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Sample GSM1942556 Query DataSets for GSM1942556
Status Public on May 01, 2016
Title Skin_Fibroblast_c149
Sample type genomic
 
Source name Skin biopsy, fibroblast, cell 149
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 0.960542 2.573485 0.9791354 0.8194934
rs10074911 NC 0 0.04882441 1.679062 0.05086227 -0.5063468
rs10084637 NC 0.005768287 0.1571847 0.3678904 0.130761 -1.391721
rs1009128 NC 0 0.9815398 1.502654 0.9958874 0.5067194
rs10111087 NC 0.02233469 0.9938336 0.2310928 0.9981942 -2.518062
rs10166589 NC 0.2200285 0.9576321 0.6693901 0.9565963 -1.168707
rs10166677 NC 0.6396135 0.9812639 0.5162379 1 0.7760068
rs10200219 NC 0.2767292 0.9833264 1.349288 1 0.3354301
rs10221474 NC 0.665179 0.09226707 0.5835117 0.03008983 -0.08212645
rs10224134 NC 0.739988 0.07570563 0.4111963 0.03453044 -1.246756
rs10232915 NC 0.4625357 0.9952367 1.138994 1 -0.09456608
rs10239194 NC 0 0.04205834 0.7552489 0.06223468 -0.818641
rs10283502 NC 0 0.1599419 2.42073 0.07326631 0.721005
rs10414884 AA 0.8318321 0.04000569 1.190269 0.01229663 0.06846242
rs10458479 NC 0 0.9551941 2.098918 0.9350937 0.5137677
rs10468635 NC 0.3845799 0.03789712 1.360949 0.002862721 0.7993168
rs10502267 AA 0.8258053 0.04708021 1.721606 0.0426775 0.1097894
rs1065426 NC 0 0.04000108 2.992281 0.003243133 1.065928
rs10737933 NC 0.0285952 0.6901804 2.029147 0.7709148 0.5524992
rs10794411 AA 0.9115698 0.02232758 0.7241929 0 0.8273476

Total number of rows: 298563

Table truncated, full table size 17673 Kbytes.




Supplementary file Size Download File type/resource
GSM1942556_9421749040_R01C01_Grn.idat.gz 1.9 Mb (ftp)(http) IDAT
GSM1942556_9421749040_R01C01_Red.idat.gz 1.9 Mb (ftp)(http) IDAT
Processed data included within Sample table

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