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Sample GSM1942555 Query DataSets for GSM1942555
Status Public on May 01, 2016
Title Skin_Fibroblast_c148
Sample type genomic
 
Source name Skin biopsy, fibroblast, cell 148
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 0.9745402 2.175181 0.994511 0.5888999
rs10074911 NC 0 0.7725148 2.465672 1 0.04797858
rs10084637 NC 0 0.1801086 0.3070865 0.1561685 -1.667788
rs1009128 NC 0 0.9897701 1.521133 1 0.5243523
rs10111087 NC 0 0.8354146 1.012013 0.836731 -0.5188863
rs10166589 NC 0.7030756 0.9834369 2.211675 0.9968015 0.5839254
rs10166677 NC 0.6396135 0.9432853 0.1189358 0.9946173 -1.346133
rs10200219 NC 0 0.78116 0.08952095 0.6440889 -3.786492
rs10221474 NC 0.665179 0.07920017 0.3249907 0.01418181 -0.9223837
rs10224134 AA 0.8310968 0.01962557 0.7838164 0 -0.2790995
rs10232915 NC 0.4625357 0.9901822 1.669806 1 0.452743
rs10239194 NC 0 0.02149801 1.680747 0.02232086 0.3354372
rs10283502 NC 0 0.05067552 2.425831 0 0.7240415
rs10414884 AA 0.7709756 0.02621336 2.510663 0.000652207 1.156494
rs10458479 NC 0 0.96588 1.903507 0.9895104 0.3727822
rs10468635 NC 0.3845799 0.04352168 0.6675911 0.01030004 -0.2339297
rs10502267 NC 0.2371972 0.6352763 1.889194 0.6832407 0.2344143
rs1065426 NC 0 0.03004404 2.369376 0 0.7291891
rs10737933 NC 0.1511156 0.7223697 1.652843 0.830361 0.262642
rs10794411 AA 0.9115698 0.03275114 0.8031559 0 0.970875

Total number of rows: 298563

Table truncated, full table size 17475 Kbytes.




Supplementary file Size Download File type/resource
GSM1942555_9402204071_R06C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942555_9402204071_R06C02_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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