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Sample GSM2309182 Query DataSets for GSM2309182
Status Public on Sep 12, 2016
Title Guthrie T-76
Sample type genomic
 
Source name Guthrie card blood
Organism Homo sapiens
Characteristics tissue: infant blood
Growth protocol LNCaP prostate cancer cells were cultured as described in PMID 11850822. Normal prostate epithelial cells (PrEC) were cultured according to the manufacturer’s instructions in prostate epithelial growth medium (PrEGM, catalogue no. CC-3166; Cambrex Bio Science) as described in PMID 20173741. Patient-matched cancer associated fibroblasts (CAFs) and non-malignant tissue associated fibroblasts (NAFs) (n=3 pairs) were isolated and validated as described in PMID 23558784
Extracted molecule genomic DNA
Extraction protocol Genomic DNA for LNCaP and PrEC cell lines was extracted using QIAamp DNA Mini and Blood Mini kit following the manufacturer’s protocol for cultured cells (Qiagen). Genomic DNA was extracted from the CAF and NAF samples using the DNeasy kit (Qiagen) with on-column RNase A digestion. Genomic DNA was extracted from the Guthrie cards using GenSolve technology (IntegenX) followed by purification using the QIAamp DNA micro kit (Qiagen) and an additional ethanol precipitation step.
Label Cy5 and Cy3
Label protocol Standard Illumina Protocol
 
Hybridization protocol Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol
Scan protocol Standard Illumina Protocol
Description infant blood from archival Guthrie cards
Data processing Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and background normalized using negative control probes to generate methylation β-values which were used for all downstream analyses.
 
Submission date Sep 12, 2016
Last update date Sep 12, 2016
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 GPL21145
Series (2)
GSE86831 Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [MethylationEPIC]
GSE86833 Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling

Data table header descriptions
ID_REF
VALUE Normalized beta-values.
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.6028783 0
cg00000103 0.9046833 0
cg00000109 0.8652314 0
cg00000155 0.8956859 0
cg00000158 0.9158093 0
cg00000165 0.08090399 0
cg00000221 0.8155115 0
cg00000236 0.7347729 0
cg00000289 0.8936689 0
cg00000292 0.7905667 0
cg00000321 0.2235571 0
cg00000363 0.2793901 0
cg00000540 0.8714552 0
cg00000579 0.9128962 0
cg00000596 0.7777095 0
cg00000622 0.008074985 0
cg00000658 0.762233 0
cg00000714 0.3031538 0
cg00000721 0.8939543 0
cg00000734 0.1071386 0

Total number of rows: 864935

Table truncated, full table size 19487 Kbytes.




Supplementary file Size Download File type/resource
GSM2309182_200134080015_R07C01_Grn.idat.gz 7.1 Mb (ftp)(http) IDAT
GSM2309182_200134080015_R07C01_Red.idat.gz 7.1 Mb (ftp)(http) IDAT
Processed data included within Sample table
Processed data are available on Series record

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