|
| Status |
Public on Apr 19, 2024 |
| Title |
WBCminusNeu_ZT19_replicate |
| Sample type |
genomic |
| |
|
| Source name |
Whole blood depleted of neutrophils
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: male
age: 52
ct: 19
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Neutrophils were isolated from whole blood by immunomagnetic negative selection with EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL) according to the manufacturer's protocol. The remaining fraction of white blood cells depleted of neutrophils were snap-frozen and stored in -80 °C before DNA extraction. DNA was extracted with NucleoSpin® Blood XL (Macherey-Nagel) using the standard protocol
|
| Label |
Cy3 and Cy5
|
| Label protocol |
Standard Infinium HD Methylation Assay protocol
|
| |
|
| Hybridization protocol |
Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Infinium HD Methylation Assay protocol
|
| Scan protocol |
Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting
|
| Description |
White blood cells left over after magnetically activated cell sorting isolation of neutrophils
|
| 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
|
| |
|
| 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 |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE247197 |
Epigenetic age oscillates during the day (WBC-Neu 52 yr old) |
| GSE247198 |
Epigenetic age oscillates during the day |
|
