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Series GSE154566 Query DataSets for GSE154566
Status Public on Dec 15, 2020
Title DNA methylation signatures of adolescent victimization: Analysis of a longitudinal monozygotic twin sample.
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium EPIC array (“EPIC array”) in DNA samples isolated from buccal swabs collected at ages 5, 10 and 18 and whole blood samples collected at age 18 from 118 Monozygotic twin pairs from the Environmental Risk (E-Risk) Longitudinal Twin Study. Comparison of DNA methylation profiles of 233 age 18 blood samples with data on EPIC and Illumina 450K methylation arrays.
 
Overall design Bisulphite converted DNA from the 944 samples were hybridised to the Illumina Infinium HumanMethylation850 BeadChip; raw data (preQC folder->raw idats folder; Phenotype_file_944preQC.csv), processed files (betas_normalised.csv, pheno.csv). Overlapping samples (N=233) had methylation data on two DNA methylation arrays -EPIC and 450K, we compared the methylation profiles of these samples to assess the correlation between the two arrays using two strategies: -(1)When these samples were normalized together (raw files for EPIC array data are in preQC folder->raw idats folder; Overlaping_probes_normalised_together_450K_EPIC_pheno.csv, raw idats for 450K are in folder raw_idats_450k, processed betas for both arrays file (Overlaping_probes_normalised_together_450K_EPIC_betas.csv) (2) When these samples were normalized separately - only overlapping probes on both arrays for the common samples were analysed - processed betas file for 450K array (Overlaping_probes_normalised_seperately_450K_betas.csv, Overlaping_probes_normalised_seperately_450K_pheno.csv) and EPIC array (Overlaping_probes_normalised_seperately_EPIC_betas.csv, Overlaping_probes_normalised_seperately_EPIC_pheno.csv). Categories description: 1 - MZ discordant twins exposed to adolescence victimisation, 2 - MZ concordant twins unexposed to adolescence victimisation, and 3 - MZ concordant twins exposed to adolescent victimisation
 
Contributor(s) Kandaswamy R, Wong CC
Citation(s) 33371772
Submission date Jul 16, 2020
Last update date Jul 06, 2022
Contact name Chloe Wong
E-mail(s) chloe.wong@kcl.ac.uk
Organization name King's College London
Street address MRC SGDP Centre, Institute of Psychiatry,
City London
State/province Select a State or Province
ZIP/Postal code SE5 8AF
Country United Kingdom
 
Platforms (2)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
GPL23976 Illumina Infinium HumanMethylation850 BeadChip
Samples (1177)
GSM4673476 1_1_10
GSM4673477 1_1_18B
GSM4673478 1_1_18C
Relations
Reanalyzed by GSE207605
BioProject PRJNA646725

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE154566_Kandaswamy_GEO.rdat 6.0 Gb (ftp)(http) RDAT
GSE154566_Overlaping_probes_normalised_seperately_450K_betas.csv.gz 572.3 Mb (ftp)(http) CSV
GSE154566_Overlaping_probes_normalised_seperately_450K_pheno.csv.gz 10.2 Kb (ftp)(http) CSV
GSE154566_Overlaping_probes_normalised_seperately_EPIC_betas.csv.gz 574.3 Mb (ftp)(http) CSV
GSE154566_Overlaping_probes_normalised_seperately_EPIC_pheno.csv.gz 2.6 Kb (ftp)(http) CSV
GSE154566_Overlaping_probes_normalised_together_450K_EPIC_betas.csv.gz 1.5 Gb (ftp)(http) CSV
GSE154566_Overlaping_probes_normalised_together_450K_EPIC_pheno.csv.gz 5.1 Kb (ftp)(http) CSV
GSE154566_Phenotype_file_944preQC.csv.gz 8.0 Kb (ftp)(http) CSV
GSE154566_RAW.tar 14.9 Gb (http)(custom) TAR (of IDAT)
GSE154566_betas_normalised.csv.gz 3.8 Gb (ftp)(http) CSV
GSE154566_pheno_INCcelltype.csv.gz 35.0 Kb (ftp)(http) CSV
Processed data are available on Series record
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