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Sample GSM4609006 Query DataSets for GSM4609006
Status Public on Feb 04, 2021
Title OAVS05
Sample type genomic
 
Source name Case
Organism Homo sapiens
Characteristics disease state: Oculo-auriculo-vertebral spectrum
tissue: Peripheral Blood
Sex: female
epigenetic age: 5.8
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from peripheral blood lymphocytes of probands and their parents (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).
Label Cy3 and Cy5
Label protocol Standard Illumina protocol
 
Hybridization protocol Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K Beadchip using standard Illumina protocol
Scan protocol Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).
Data processing Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP (release 2.8.9) package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). ChAMP pre-processing module appears more suitable in preventing biases due to genetic variations in downstream analyses by filtering an increased number of probes. Sites with a detection p-value above 0.01 (n=4706) and a bead count <3 in at least 5% of samples (n=226) were removed. Moreover, also non-GpG probes (n=3025), potentially SNP affected probes (n=57699) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9705) were filtered out. As a final outcome of the filtering procedures, a total of 410140 CpG sites were retained. Quantile normalization was performed through preprocessCore package (release 1.38.1).
 
Submission date Jun 10, 2020
Last update date Feb 04, 2021
Contact name Luciano Calzari
Organization name IRCCS Istituto Auxologico Italiano
Lab Bioinformatics and Statistical Genomics Unit
Street address Via Zucchi 18
City Cusano Milanino
State/province MI
ZIP/Postal code 20095
Country Italy
 
Platform ID GPL13534
Series (1)
GSE152204 Genome-wide DNA methylation analysis of a cohort of 41 patients affected by Oculo-auriculo-vertebral spectrum (OAVS).

Data table header descriptions
ID_REF
VALUE Normalized (Quantile) average beta
OAVS05_Detection_Pval

Data table
ID_REF VALUE OAVS05_Detection_Pval
cg00000029 0.578708479956948 0
cg00000109 0.802099755495378 0
cg00000165 0.221855717202615 0
cg00000236 0.778833989458163 0
cg00000289 0.635361038049028 0
cg00000292 0.817022996125679 0
cg00000321 0.278497714230336 0
cg00000363 0.383925141144326 0
cg00000658 0.780470979967339 0
cg00000714 0.270187400426409 0
cg00000721 0.85136245217069 0
cg00000734 0.102563414771951 0
cg00000769 0.051474154059078 0
cg00000807 0.833928100105394 0
cg00000884 0.801429712508573 0
cg00000905 0.123180024326289 0
cg00000924 0.528343303372133 0
cg00000948 0.845703664378378 0
cg00000957 0.879578333988485 0
cg00001099 0.791200831871972 0

Total number of rows: 409978

Table truncated, full table size 12467 Kbytes.




Supplementary file Size Download File type/resource
GSM4609006_200107460090_R05C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM4609006_200107460090_R05C01_Red.idat.gz 4.0 Mb (ftp)(http) IDAT
Processed data included within Sample table

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