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Status |
Public on Apr 19, 2024 |
Title |
Neu30yo_ZT11_replicate1 |
Sample type |
genomic |
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Source name |
Neutrophils
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Organism |
Homo sapiens |
Characteristics |
Sex: male age: 30 ct: 11
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Extracted molecule |
genomic DNA |
Extraction protocol |
Immediately after collection, the blood samples were processed using Optilyse C™ (Beckman Coulter, CA, USA), both for erythrolysis and mild fixation of the blood cells. These samples were then subsequently sorted for neutrophils via fluorescence activated cell sorting (FACS) using CD15-APC, CD16-PE, and CD45- PE-Cy™7 (BD Pharmingen™, NJ, USA). The neutrophil samples were snap-frozen and stored in -80 °C before DNA extraction.DNA was extracted with NucleoSpin® Tissue kit using the standard protocol
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Label |
Cy3 and Cy5
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Label protocol |
Standard Infinium HD Methylation Assay protocol
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Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylationEPIC v1.0 Beadchip using standard Infinium HD Methylation Assay protocol
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Scan protocol |
Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting
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Description |
Neutrophils purified with fluorescence activated cell sorting
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Data processing |
Processeing was done using the R “minfi” package. First, all samples having more than 3% of probes with poor detection p-values (detection p < 0.05) using an alternative detection p-value approach(Heiss and Just 2019) were removed as outliers. Then array normalization was performed using “noob” background correction followed by functional normalization, and signals from the methylated and unmethylated channels were combined to obtain the methylation beta values. Additional outliers were identified by measuring Pearson’s correlations among all the sample pairs and removing samples with an average inter-sample correlation value more than three standard deviations below the mean. Finally, for the datasets that contained technical replicates for every sample, all the samples with only a single replicate remaining after quality control were discarded. R "minfi" package computed Average Beta values after "noob" background correction and "functional" normalization
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Submission date |
Nov 07, 2023 |
Last update date |
Apr 19, 2024 |
Contact name |
Karolis Koncevičius |
E-mail(s) |
karolis.koncevicius@gmc.vu.lt
|
Organization name |
Vilnius University
|
Department |
Institute of Biotechnology, Life Sciences Center
|
Lab |
Laboratory of Epigenomic Studies
|
Street address |
Saulėtekio al. 7
|
City |
Vilnius |
ZIP/Postal code |
10257 |
Country |
Lithuania |
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|
Platform ID |
GPL21145 |
Series (2) |
GSE247193 |
Epigenetic age oscillates during the day (Neu 30 yr old) |
GSE247198 |
Epigenetic age oscillates during the day |
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