|
| Status |
Public on Nov 23, 2023 |
| Title |
X2043 [Control] |
| Sample type |
genomic |
| |
|
| Source name |
Control
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole Blood
Sex: female
disease state: Control
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted from peripheral blood lymphocytes (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, 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 package (Morris TJ et al., 2014) implemented R environment (version 3.6.2). Sites with a detection p-value above 0.01 (n=4761) and a bead count <3 in at least 5% of samples (n=250) were removed. Moreover, also non-CpG probes (n=3051), potentially SNP affected probes (n=57628) (Zhou Wet al., 2017) probes aligning to multiple locations (n=11) (Nordlund J et al., 2013) and of X and Y chromosomes (n=9718) were filtered out. As a final outcome of the filtering procedures, a total of 410093 CpG sites were retained.
ChAMP loading, Normalization (SWAN) and Batch Correction (ComBat)
|
| |
|
| Submission date |
Aug 02, 2023 |
| Last update date |
Nov 23, 2023 |
| 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) |
| GSE239901 |
Exploring Epigenetic Drift and Rare Epivariations in Amyotrophic Lateral Sclerosis by an Epigenome-Wide Association Study |
|
