NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1942053 Query DataSets for GSM1942053
Status Public on May 01, 2016
Title Fibroblast_S1_c11_sc2
Sample type genomic
 
Source name Primary fibroblast cell line S1, cell 11, 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 0.1128014 0.8975143 0.7570916 0.9099058 -0.9984947
rs10074911 NC 0 0.1512728 2.848903 0.2424077 0.2564041
rs10084637 NC 0.5911415 0.0901114 0.5402045 0.05642083 -0.7913561
rs1009128 NC 0 0.963823 0.9067633 0.9798409 -0.2219959
rs10111087 NC 0 0.265325 0.4185835 0.2519979 -1.926397
rs10166589 NC 0.7030756 0.9746544 2.500329 0.9831179 0.7511709
rs10166677 NC 0.5024343 0.887983 0.2736798 0.8921087 -0.1500482
rs10200219 NC 0.1584068 0.4866512 0.7321659 0.0640852 -0.9539125
rs10221474 NC 0.07603905 0.1571467 0.3602971 0.1090761 -0.7979179
rs10224134 AA 0.8310968 0.03051976 1.179908 0 0.3037309
rs10232915 NC 0.4625357 0.9929332 1.5939 1 0.3881316
rs10239194 NC 0 0.03696869 0.8347472 0.05235413 -0.6742539
rs10283502 NC 0 0.08358212 0.6117085 0 -1.263521
rs10414884 AA 0.8318321 0.01454007 1.841098 0 0.7185836
rs10458479 NC 0 0.9557888 1.817758 0.9381223 0.3062817
rs10468635 NC 0.3845799 0.06080443 0.7764267 0.03315294 -0.03333112
rs10502267 BB 0.8255532 0.9332239 2.081563 0.9618331 0.611742
rs1065426 NC 0 0.08122497 2.392139 0.04565815 0.7429835
rs10737933 NC 0 0.6724513 2.525141 0.7381732 0.8646588
rs10794411 AA 0.8142213 0.10559 0.1453122 0.05455908 -1.535396

Total number of rows: 298563

Table truncated, full table size 17881 Kbytes.




Supplementary file Size Download File type/resource
GSM1942053_8907686167_R03C01_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942053_8907686167_R03C01_Red.idat.gz 2.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap