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Sample GSM2279235 Query DataSets for GSM2279235
Status Public on Mar 26, 2018
Title HumanOmni2.5 NPF3
Sample type genomic
 
Source name NPF
Organism Homo sapiens
Characteristics patient: 3
gender: Male
tissue: Prostate
cell type: Normal Prostate Fibroblast
Treatment protocol Cells were cultured in standard media to approximately 80% confluency before being trypsinised, resuspended in media and then centrifuged to create cell pellets. Cells were stored at -80°C until DNA extraction.
Growth protocol Prostate tissue was chopped into small pieces, approximately 2 mm3, and digested overnight at 37°C in RPMI containing 10% fetal calf serum (FCS), 25 mM HEPES, 100 U/mL penicillin, 100 mg/mL streptomycin, 0.5 mg/mL fungizone, 100 mg/mL gentamicin, 225 U/mL Collagenase Type I and 125 U/mL Hyaluronidase Type II (Sigma Aldrich) as previously described [PMID: 23558784]. Cell suspensions were seeded in RPMI containing 5% FCS, penicillin/streptomycin, 1 nM testosterone (Sigma Aldrich) and 10 ng/mL bFGF (Millipore), a medium that selects for fibroblasts compared to other prostatic cell types. Cells were grown at 37°C in a humidified incubator with 5% O2 and 5% CO2. The first passage of cells typically reached confluency within 2 weeks. The cells were used between passages 2-6.
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from CAF and NPF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Eluates were precipitated with 0.1 volume sodium acetate and 2.5 volumes ethanol and then resuspended in nuclease-free water. DNA was quantified using a NanoDrop 2000. 200ng of DNA was quantified using the Illumina HumanOmni2.5-8 Beadchip (Illumina, CA, USA)
Label biotin
Label protocol Standard Illumina Protocol
 
Hybridization protocol Standard Illumina Protocol
Scan protocol Standard Illumina Protocol
Description NPF3
Data processing Copy numbers were estimated using circular binary segmentation (CBS) [PMID: 15475419] to translate intensity measurements into regions of equal copy number. The raw array data was processed using crlmm (v1.25.1) [PMID: 19661241] for background correction and normalization, accounting for batch effects.The resulting log R ratios were then smoothed to remove outliers prior to segmentation (R package DNAcopy). All analyses were carried out in R3.1.2 (www.r-project.org).
Tab delimited text files - LogR ratio (LRR), B allele frequency (BAF) and genotype calls (1=AA, 2=AB, 3=BB)
 
Submission date Aug 15, 2016
Last update date Mar 26, 2018
Contact name Ruth Pidsley
E-mail(s) r.pidsley@garvan.org.au
Organization name Garvan Institute of Medical Research
Street address 384 Victoria Street
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
 
Platform ID GPL16104
Series (2)
GSE85605 Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype [Illumina_Omini 2.5-8_SNP]
GSE86260 Cancer Associated Fibroblasts are defined by a core set of epigenome changes that contribute to the tumor phenotype

Supplementary file Size Download File type/resource
GSM2279235_HumanOmni2.5_NPF3_Grn.idat.gz 16.0 Mb (ftp)(http) IDAT
GSM2279235_HumanOmni2.5_NPF3_Red.idat.gz 16.4 Mb (ftp)(http) IDAT
Processed data are available on Series record

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