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Sample GSM2644998 Query DataSets for GSM2644998
Status Public on Jan 01, 2018
Title Normal_28
Sample type genomic
 
Source name Self-sample HPV-positive control_28
Organism Homo sapiens
Characteristics disease state: Normal
sample type: Self-sampled cervico-vaginal material (self-sample)
Extracted molecule genomic DNA
Extraction protocol DNA from self-samples was isolated using the NucleoMag 96 Tissue kit (Macherey-Nagel, Düren, Germany) and a Microlab Star robotic system (Hamilton, Martinsried, Germany) according to the manufacturer’s protocol. Isolated DNA was bisulphite-converted using the EZ DNA Methylation kit (Zymo Research, Orange, CA, USA) according to manufacturer's instructions.
Label Cy3 en Cy5
Label protocol Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
 
Hybridization protocol Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
Scan protocol Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
Description Lavage-based self-sample
Data processing Data were pre-processed, including probe quality control. Probes which, (i) showed a low bead count (<3 in at least 5% of samples), (ii) had a detection p-value of > 0.05 in at least 3% of samples, (iii) contained SNPs at or within 10 bp from the target CpG-site (Chen et al. Epigenetics 2013), (iv) were vulnerable to cross-hybridization (Chen et al. Epigenetics 2013) or (v) were located on allosomes, were removed, leaving 365,620 probes for analysis. Data were normalised using dasen normalisation (Pidsley et al. BMC Genomics 2013), which uses a different background correction and quantile normalisation for type I and type II probes. It returns normalised beta-values, representing methylation percentage at the corresponding CpG-site.
 
Submission date May 31, 2017
Last update date Jan 23, 2018
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 (1)
GSE99511 Identification and validation of a novel 3-gene methylation classifier for HPV-based cervical screening on self-samples

Data table header descriptions
ID_REF
VALUE Normalized (provided the normalization method) Average Beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00000029 0.269575456 0
cg00000165 0.207599188 0
cg00000236 0.874934063 0
cg00000289 0.735384329 0
cg00000321 0.397768094 0
cg00000363 0.240982526 0
cg00000622 0.045487275 0
cg00000658 0.834412815 0
cg00000714 0.140553258 0
cg00000721 0.922201931 0
cg00000734 0.114366264 0
cg00000769 0.115534158 0
cg00000807 0.911878525 0
cg00000884 0.883583632 0
cg00000905 0.132497339 0
cg00000948 0.906114875 0
cg00001099 0.834296414 0
cg00001245 0.055389907 0
cg00001249 0.782564879 0
cg00001269 0.876287076 0

Total number of rows: 365620

Table truncated, full table size 8895 Kbytes.




Supplementary file Size Download File type/resource
GSM2644998_9828653103_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM2644998_9828653103_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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