|
| Status |
Public on Apr 22, 2022 |
| Title |
peripheral blood (9989536146_R06C01) |
| Sample type |
genomic |
| |
|
| Source name |
peripheral blood
|
| Organism |
Homo sapiens |
| Characteristics |
case (panic disorder (1), control(0)): 1
weighted life events: 40
tissue: peripheral blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was extracted from peripheral blood
|
| Label |
Cy3, Cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using standard recommended Illumina scanner setting
|
| Data processing |
The Bioconductor R package minfi was used for the quality control of DNAm data. Failed probes based on a detection P-value larger than 0.01 in >50% of the samples as well and non-specific binding probes a nd probes on X and Y chromosome were removed.
We also excluded probes if single nucleotide polymorphisms (SNPs) were documented in the interval for which the Illumina probe is designed to hybridize. Probes located close (10 bp from query site) to a SNP which had a minor allele frequency of ≥0.05, as reported in the 1,000 Genomes Project, were also removed
The data were then normalized with functional normalization. Batch effects were identified using the Empirical Bayes’ method ComBat . Batch corrected M-values after ComBat were used for all further statistical analyses
|
| |
|
| Submission date |
Apr 18, 2022 |
| Last update date |
Apr 22, 2022 |
| Contact name |
Binder Elisabeth |
| E-mail(s) |
binder@psych.mpg.de
|
| Organization name |
Max-Planck-Institute Psychiatry
|
| Street address |
Kraepelinstr. 2+10
|
| City |
Munich |
| ZIP/Postal code |
80804 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE200954 |
Epigenome-wide association analysis on weighted life events in PD patients - discovery cohort |
| GSE201016 |
Effects of stressful life-events on DNA methylation in panic disorder and major depressive disorder |
|
