|
| Status |
Public on Feb 04, 2021 |
| Title |
OAVS08 |
| Sample type |
genomic |
| |
|
| Source name |
Case
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Oculo-auriculo-vertebral spectrum
tissue: Peripheral Blood
Sex: male
epigenetic age: 11.7
|
| 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). |
|
