|
| Status |
Public on Jun 21, 2022 |
| Title |
gDNA_WB_B6_T1 |
| Sample type |
genomic |
| |
|
| Source name |
Whole blood
|
| Organism |
Mus musculus |
| Characteristics |
age (weeks): 117
Sex: female
strain: C57BL/6
sample type: Whole blood
condition: healthy
dataset: B6 training
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from whole blood samples (taken by submandibular bleeding or post mortem from vena cava or heart) using the QIAamp® DNA Mini and Blood Mini kit (Qiagen GmbH, Hilden, Germany), according to manufacturer's instructions
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA (EZ DNA Methylation Kit, Zymo Research, CA, USA) was amplified, fragmented and hybridised to Illumina Infinium MouseMethylation BeadChip using standard Illumina protocol
|
| Scan protocol |
The array samples were scanned with the iScan System
|
| Description |
Healthy whole blood sample, training set
|
| Data processing |
The three different datasets (B6 training, B6 validation and DBA) were processed separately. The raw data from IDAT files was read and processed in R with the ENmix package, and the betas were normalized using the ENmixD method (ENmix background correction and RELIC dye-bias normalization). Probes with detection p-values > 0.01 or more than 10% of NA values were filtered out. One sample with more than 10% missing values was not considered for further analysis. Furthermore, CpGs on X and Y chromosomes were not considered for epigenetic clocks. Probe-type bias adjustment was performed with the Regression on Correlated Probes method
Normalized beta values (ENmixD normalization) with probe-type bias adjustment (Regression on Correlated Probes method)
|
| |
|
| Submission date |
Apr 09, 2022 |
| Last update date |
Nov 14, 2022 |
| Contact name |
Wolfgang Wagner |
| E-mail(s) |
wwagner@ukaachen.de
|
| Phone |
+49 241 8088611
|
| Organization name |
RWTH Aachen University
|
| Department |
Helmholtz Institute for Biomedical Engineering
|
| Lab |
Stem Cell Biology and Cellular Engineering
|
| Street address |
Pauwelsstrasse 20
|
| City |
Aachen |
| ZIP/Postal code |
52074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL31950 |
| Series (1) |
| GSE200527 |
Genome wide DNA methylation profiling of whole blood samples from C57BL/6 and DBA/2J healthy mice |
|
