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Sample GSM1942075 Query DataSets for GSM1942075
Status Public on May 01, 2016
Title Fibroblast_S1_c29_sc2
Sample type genomic
 
Source name Primary fibroblast cell line S1, cell 29, sister cell 2
Organism Homo sapiens
Characteristics gender: Female
cell line: S1
Treatment protocol Single fibroblasts were plated separately and the two cells that derived following a cell division were isolated individually.
Growth protocol Primary fibroblasts were grown in 75-cm2 plastic flasks (BD Falcon, USA) under standard culture conditions in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12) (Gibco, USA) medium complemented with 10% Fetal Bovine Serum (FBS) (Thermo Scientific, USA).
Extracted molecule genomic DNA
Extraction protocol The genome of collected single cells was amplified using either Genomiphi V2 (GE Healthcare, UK) or RepliG-sc (Qiagen, NL) whole genome amplification kit.
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 16, 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)
GSE75068 Segmental chromosomal imbalances arise at high frequency in human fibroblasts (S1)
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 0.6774432 0.9203272 1.889702 0.9349635 0.3400143
rs10074911 NC 0 0.4730011 2.326411 0.939893 -0.03589679
rs10084637 NC 0.6409112 0.07943168 0.8423359 0.04458404 -0.142982
rs1009128 NC 0 0.9877009 1.047796 1 -0.01343661
rs10111087 NC 0 0.4773784 0.1211162 0.4713892 -3.810562
rs10166589 NC 0.7030756 0.9859855 1.648004 1 0.1623423
rs10166677 NC 0.6396135 0.9707952 0.2631535 1 -0.1973075
rs10200219 NC 0.2767292 0.2160837 2.006926 0 0.3578894
rs10221474 NC 0.665179 0.1016011 0.4206225 0.04145338 -0.5572882
rs10224134 AA 0.8301451 0.06083463 0.543811 0.02040956 -0.8337671
rs10232915 NC 0.4625357 0.9851482 1.435721 0.9983195 0.2302594
rs10239194 NC 0 0.01486222 1.335888 0.009438776 0.004133523
rs10283502 NC 0 0.0761628 2.387761 0 0.7012209
rs10414884 AA 0.8318321 0.03123482 1.045745 0.004891669 -0.1111487
rs10458479 NC 0 0.9674055 1.803296 0.9972786 0.2947583
rs10468635 NC 0.3845799 0.03553613 1.437706 0 0.8808601
rs10502267 BB 0.8258053 0.9538375 0.9562455 0.9811077 -0.4925046
rs1065426 NC 0 0.9814354 1.38872 0.9956821 -0.04156234
rs10737933 NC 0.444411 0.4986581 1.000065 0.4431665 -0.4776639
rs10794411 AA 0.9115698 0.01890312 0.5906935 0 0.5352869

Total number of rows: 298563

Table truncated, full table size 17612 Kbytes.




Supplementary file Size Download File type/resource
GSM1942075_9297203151_R06C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942075_9297203151_R06C02_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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