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Sample GSM1942646 Query DataSets for GSM1942646
Status Public on May 01, 2016
Title Skin_Fibroblast_c167
Sample type genomic
 
Source name Skin biopsy, fibroblast, cell 167
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)
GSE75098 Segmental chromosomal imbalances arise at high frequency in human fibroblasts (SB_sc_2)
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 0.9706619 2.052934 0.9902511 0.5021187
rs10074911 NC 0 0.8083097 2.000351 1 -0.2537494
rs10084637 NC 0.6409326 0.0645003 0.7793256 0.02803498 -0.2446225
rs1009128 NC 0 0.9816902 1.22533 0.9960236 0.212377
rs10111087 NC 0.005982787 0.9332473 0.1428147 0.9364436 -3.264109
rs10166589 NC 0.7030756 0.9769097 1.626287 0.9866318 0.1331281
rs10166677 NC 0.6396135 0.9640629 0.1932193 1 -0.6437336
rs10200219 NC 0.2767292 0.9806005 1.308058 0.9997629 0.2876435
rs10221474 NC 0.665179 0.04328518 1.057729 0 0.7914622
rs10224134 AA 0.8310968 0.03909261 1.256126 0 0.3883538
rs10232915 NC 0.4625357 0.9930648 1.205607 1 -0.0145495
rs10239194 NC 0 0.02509083 1.42334 0.0292956 0.09561545
rs10283502 NC 0 0.1639613 2.558442 0.07782309 0.8008279
rs10414884 AA 0.8318321 0.02109155 1.666547 0 0.5694888
rs10458479 NC 0 0.9629963 1.819799 0.9748254 0.3079011
rs10468635 NC 0.3845799 0.05109869 0.6302481 0.02031908 -0.3245787
rs10502267 NC 0.03481701 0.1982739 0.7577772 0.2189649 -1.132426
rs1065426 NC 0 0.04139151 2.507775 0.004673739 0.8110899
rs10737933 NC 0.4460516 0.5870154 1.094341 0.580393 -0.3575847
rs10794411 AA 0.9115698 0.03012156 0.5638539 0 0.4619718

Total number of rows: 298563

Table truncated, full table size 17587 Kbytes.




Supplementary file Size Download File type/resource
GSM1942646_9402204022_R06C01_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942646_9402204022_R06C01_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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