NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1942074 Query DataSets for GSM1942074
Status Public on May 01, 2016
Title Fibroblast_S1_c29_sc1
Sample type genomic
 
Source name Primary fibroblast cell line S1, cell 29, 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 0.02264503 0.8152596 0.7508387 0.8195573 -1.076588
rs10074911 NC 0 0.8981392 2.043272 1 -0.2231209
rs10084637 NC 0.6409326 0.07455362 0.7751732 0.03917749 -0.2594276
rs1009128 NC 0 0.9695652 0.4488896 0.9850417 -1.236361
rs10111087 NC 0.3764983 0.989413 0.5930564 0.9936886 -1.162202
rs10166589 NC 0.7030756 0.9835522 1.390086 0.9969811 -0.08591164
rs10166677 NC 0.6396135 0.9472201 0.2041811 1 -0.5660238
rs10200219 NC 0.2767292 0.4386663 1.211757 0 -0.253461
rs10221474 NC 0.665179 0.06201047 1.047393 0 0.7713684
rs10224134 AA 0.8310968 0.07626417 0.7286937 0.0350608 -0.4216342
rs10232915 NC 0.4625357 0.9886134 1.375678 1 0.1717766
rs10239194 NC 0 0.01775295 1.605012 0.01505057 0.2689193
rs10283502 NC 0 0.218344 2.304868 0.1394768 0.6502464
rs10414884 AA 0.8318321 0.02828224 1.810373 0.002398896 0.6830195
rs10458479 NC 0 0.967433 1.578644 0.9974188 0.1028079
rs10468635 NC 0.3845799 0.05173827 0.4651705 0.0211648 -0.763379
rs10502267 NC 0.06849026 0.8897236 0.5618502 0.9211587 -1.314864
rs1065426 NC 0 0.7442073 1.452031 0.7392874 0.02275402
rs10737933 NC 0 0.4108402 2.363024 0.3318237 0.7986963
rs10794411 NC 0 0.1927126 0.09003069 0.1298861 -2.272211

Total number of rows: 298563

Table truncated, full table size 17678 Kbytes.




Supplementary file Size Download File type/resource
GSM1942074_9297203151_R05C02_Grn.idat.gz 2.0 Mb (ftp)(http) IDAT
GSM1942074_9297203151_R05C02_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