NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1942458 Query DataSets for GSM1942458
Status Public on May 01, 2016
Title Fibroblast_S2_c37_sc2
Sample type genomic
 
Source name Primary fibroblast cell line S2, cell 37, sister cell 2
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 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)
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 AB 0.8365396 0.4760436 2.029051 0.4521275 0.1679014
rs10074911 NC 0 0.2527409 2.070928 0.4321203 -0.2037251
rs10084637 NC 0.6409326 0.04127682 1.506286 0.002295422 0.7226052
rs1009128 NC 0 0.9848995 0.9888882 0.9989303 -0.09691446
rs10111087 AB 0.8685128 0.450529 2.206778 0.4436108 0.3886088
rs10166589 NC 0.7030756 0.9875285 1.668464 1 0.1818632
rs10166677 NC 0.6396135 0.9551232 0.2560121 1 -0.2387694
rs10200219 NC 0.2767292 0.9834196 1.020367 1 -0.06757697
rs10221474 NC 0.665179 0.09329528 0.4227181 0.03134159 -0.5475148
rs10224134 AA 0.8310968 0.05837429 1.822156 0.01807332 0.9123151
rs10232915 NC 0.4625357 0.9945699 1.064489 1 -0.1927741
rs10239194 NC 0 0.03063268 0.587035 0.04005402 -1.182147
rs10283502 NC 0 0.09188726 1.994863 0 0.4418521
rs10414884 NC 0.7185048 0.04804957 0.5614822 0.01908782 -1.022034
rs10458479 NC 0 0.9691424 1.562867 1 0.08831692
rs10468635 NC 0.3845799 0.04499973 0.6970777 0.01225447 -0.1730615
rs10502267 BB 0.8258053 0.9567568 1.51312 0.9838373 0.1721319
rs1065426 NC 0 0.07590944 2.312315 0.04018904 0.69402
rs10737933 NC 0.3795705 0.203896 1.82383 0.06944304 0.5131354
rs10794411 BB 0.9115698 0.9816173 0.6990748 1 0.4217377

Total number of rows: 298563

Table truncated, full table size 17749 Kbytes.




Supplementary file Size Download File type/resource
GSM1942458_9297203129_R01C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942458_9297203129_R01C02_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