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Sample GSM1942064 Query DataSets for GSM1942064
Status Public on May 01, 2016
Title Fibroblast_S1_c20_sc1
Sample type genomic
 
Source name Primary fibroblast cell line S1, cell 20, sister cell 1
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 0.1399573 0.6962731 0.7714468 0.6888626 -1.128118
rs10074911 NC 0 0.324723 3.20759 0.5853137 0.4274873
rs10084637 NC 0.4833641 0.09875598 0.5623979 0.06600197 -0.7393001
rs1009128 NC 0 0.9517257 0.8326585 0.9688841 -0.344997
rs10111087 NC 0.5412514 0.350187 2.046716 0.3397965 0.3245377
rs10166589 NC 0.7030756 0.9810326 1.727366 0.9930553 0.2246889
rs10166677 NC 0.6337203 0.9024312 0.3286524 0.91889 0.1156481
rs10200219 NC 0.2767292 0.3461286 1.514887 0 0.01905161
rs10221474 NC 0.665179 0.1022075 0.7187865 0.0421916 0.2155594
rs10224134 AA 0.8310968 0.03175371 0.8062406 0 -0.2464805
rs10232915 NC 0.4625357 1 0.8646047 1 -0.4878538
rs10239194 NC 0 0.03146002 0.8915122 0.04166013 -0.5793388
rs10283502 NC 0 0.07240568 0.7213703 0 -1.025625
rs10414884 AA 0.8318321 0.01639063 1.753783 0 0.6469626
rs10458479 NC 0 0.9563164 1.556573 0.9408091 0.08249505
rs10468635 NC 0.3845799 0.06441673 0.4543036 0.03792947 -0.8101112
rs10502267 BB 0.819567 0.9299877 1.894122 0.9588072 0.4728042
rs1065426 NC 0 0.5520877 2.211676 0.5316456 0.6298218
rs10737933 NC 0 0.3578686 0.9740338 0.264662 -0.4578496
rs10794411 AA 0.9115698 0.01885428 0.9132974 0 1.163989

Total number of rows: 298563

Table truncated, full table size 17950 Kbytes.




Supplementary file Size Download File type/resource
GSM1942064_9297950008_R02C01_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942064_9297950008_R02C01_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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