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Sample GSM2071074 Query DataSets for GSM2071074
Status Public on Feb 09, 2017
Title EK074p5
Sample type genomic
 
Source name primary human foreskin keratinocytes donor 1
Organism Homo sapiens
Characteristics cell type: primary human foreskin keratinocytes
transformation stage: normal
Treatment protocol No treatment was performed
Growth protocol Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines and isolation and culture of primary human foreskin keratinocytes (HFKs) were described previously (Steenbergen et al, Oncogene 1996). The human cervical carcinoma cell lines SiHa, HeLa and CaSki were obtained from the American Type Culture Collection (Manassas, VA, USA) and cultured as described previously (Steenbergen et al, J Natl Cancer Inst 2001).
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated using the PurelinkTM Genomic DNA Minikit (Life Technologies) following the manufacturer's instructions. 500ng double stranded DNA was bisulfite converted using the EZ DNA Methylation kit (D5002, Zymo Research) according to the manufacturer's instructions.
Label Cy3 and Cy5
Label protocol Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
 
Hybridization protocol Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
Scan protocol Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)
Data processing Data was processed and normalised using the pipeline described by Touleimat and Tost, which takes into account the different chemistry of class I and class II probes and returns Beta values representing the percentage of methylation for that particular CpG dinucleotide (Touleimat and Tost, Epigenomics 2012)
 
Submission date Feb 24, 2016
Last update date Feb 09, 2017
Contact name Daoud Sie
E-mail(s) d.sie@vumc.nl
Phone +31 20 4442428
Organization name Vrije Universiteit Medical Center
Department Pathology
Lab Microarray Core Facility
Street address De Boelelaan 1117
City Amsterdam
ZIP/Postal code 1081 HV
Country Netherlands
 
Platform ID GPL13534
Series (2)
GSE78277 Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [methylation-Illumina]
GSE78279 Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence

Data table header descriptions
ID_REF
VALUE Average Beta or normalized (provide the normalization method) Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.122143946 0
cg00000108 0.976996176 0
cg00000109 0.907550062 0
cg00000165 0.255835072 0
cg00000236 0.872665999 0
cg00000289 0.640669313 0
cg00000292 0.676630443 0
cg00000321 0.478212593 0
cg00000363 0.121124935 0
cg00000622 0.053739579 0
cg00000658 0.861029601 0
cg00000714 0.183435966 0
cg00000721 0.974717428 0
cg00000734 0.053696145 0
cg00000769 0.261211056 0
cg00000807 0.898821402 0
cg00000884 0.858017187 0
cg00000905 0.076797088 0
cg00000924 0.5320199 0
cg00000948 0.914607072 0

Total number of rows: 485577

Table truncated, full table size 11814 Kbytes.




Supplementary file Size Download File type/resource
GSM2071074_8655685078_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM2071074_8655685078_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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