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Sample GSM1942467 Query DataSets for GSM1942467
Status Public on May 01, 2016
Title Fibroblast_S2_c53_sc1
Sample type genomic
 
Source name Primary fibroblast cell line S2, cell 53, sister cell 1
Organism Homo sapiens
Characteristics gender: Female
cell line: S2
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 RepliG-sc 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)
GSE75088 Segmental chromosomal imbalances arise at high frequency in human fibroblasts (S2)
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 0.7078923 0.3958648 1.092248 0.3726355 -0.6875024
rs10074911 NC 0 0.4159222 2.475926 0.8033994 0.05396564
rs10084637 NC 0.6409326 0.0497874 1.358956 0.01172805 0.5680293
rs1009128 NC 0 0.9823843 0.9683949 0.9966523 -0.1271265
rs10111087 AB 0.8685128 0.4867934 1.750941 0.48113 0.03902613
rs10166589 NC 0.7030756 0.9847758 1.335995 0.9988875 -0.1418098
rs10166677 NC 0.6396135 0.9694588 0.484587 1 0.6833923
rs10200219 NC 0.2767292 0.9830389 0.9750797 1 -0.1334943
rs10221474 NC 0.665179 0.05361388 0.7755746 0 0.3405579
rs10224134 AA 0.8310968 0.05949559 0.7063067 0.01913806 -0.4556999
rs10232915 NC 0.4625357 0.9879605 1.260709 1 0.04527507
rs10239194 NC 0 0.008076249 1.543762 0 0.2127856
rs10283502 NC 0 0.05534376 1.681732 0 0.1955107
rs10414884 AA 0.8318321 0.03260066 1.14438 0.006044799 0.01777045
rs10458479 NC 0 0.950446 1.660285 0.910915 0.1755524
rs10468635 NC 0.3845799 0.03171467 1.328324 0 0.7705703
rs10502267 BB 0.8258053 0.9605778 1.253432 0.9874101 -0.09614996
rs1065426 NC 0 0.84484 0.8390201 0.8480506 -0.7685406
rs10737933 NC 0.3677639 0.2052258 1.640539 0.07112905 0.3597504
rs10794411 NC 0.0357633 0.1573972 0.680576 0.09935205 0.6645849

Total number of rows: 298563

Table truncated, full table size 17677 Kbytes.




Supplementary file Size Download File type/resource
GSM1942467_3998593114_R05C01_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942467_3998593114_R05C01_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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