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Sample GSM1942554 Query DataSets for GSM1942554
Status Public on May 01, 2016
Title Skin_Fibroblast_c147
Sample type genomic
 
Source name Skin biopsy, fibroblast, cell 147
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 NC 0.03785831 0.9097369 0.4289459 0.923331 -1.808077
rs10074911 NC 0 0.2833544 2.471455 0.4893576 0.05135815
rs10084637 NC 0.02763265 0.1442211 0.4593542 0.1163929 -1.062588
rs1009128 NC 0 0.9844704 1.214153 0.9985417 0.1991559
rs10111087 NC 0 0.6156173 0.07443465 0.6127101 -4.448626
rs10166589 NC 0.7030756 0.9798416 1.656019 0.9911999 0.1625127
rs10166677 NC 0.6396135 0.9704933 0.2355043 1 -0.3574933
rs10200219 NC 0.2767292 0.9868306 1.248995 1 0.227885
rs10221474 NC 0.6650106 0.1081838 0.4363237 0.04946736 -0.5064753
rs10224134 AA 0.8310968 0.04066256 1.669019 0.001255009 0.7973339
rs10232915 NC 0.4625357 0.9875334 1.658758 1 0.4407546
rs10239194 NC 0 0.061108 0.8306853 0.09921584 -0.6812913
rs10283502 NC 0 0.1106573 2.687655 0.01739222 0.8719106
rs10414884 NC 0.4645993 0.0676624 0.4425797 0.0356463 -1.381116
rs10458479 NC 0 0.9715973 1.770481 1 0.2682636
rs10468635 NC 0.3845799 0.0602613 0.7211814 0.03243476 -0.1392784
rs10502267 AA 0.8258053 0.01085822 2.379475 0.000443731 0.5910038
rs1065426 NC 0 0.04247512 1.425216 0.005788658 -0.004137811
rs10737933 NC 0 0.285973 0.7954379 0.1735069 -0.7196032
rs10794411 NC 0 0.2715742 0.09618911 0.1980706 -2.21729

Total number of rows: 298563

Table truncated, full table size 17598 Kbytes.




Supplementary file Size Download File type/resource
GSM1942554_9402204071_R05C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942554_9402204071_R05C02_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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