DNA Methylation (EPIC) from the Grady Trauma Project
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ABSTRACT:
PROVIDER: PRJNA546502 | ENA |
REPOSITORIES: ENA
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Project description:Childhood and cumulative exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in whole blood, with the goal of identifying associaitons between peripheral DNA methylation and psychiatric symptoms.
2019-06-06 | GSE132203 | GEO
Project description:Childhood and cumulative exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in whole blood from African American participants, with the goal of identifying associaitons between peripheral DNA methylation and psychiatric symptoms. DNA methylation was assessed in whole blood from participants of the Grady Trauma Project. Blood was collected in EDTA vacuum tubes prior to extraction. DNA methylation was interrogated for each sample using the HumanMethylation450 BeadChip (Illumina).
2015-09-03 | E-GEOD-72680 | biostudies-arrayexpress
Project description:Childhood and cumulative exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in whole blood from African American participants, with the goal of identifying associaitons between peripheral DNA methylation and psychiatric symptoms.
2015-09-03 | GSE72680 | GEO
Project description:DNA methylation analysis in oropharyngeal cancer [EPIC array]
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Project description:Infinium® HumanMethylation450 BeadChip and EPIC arrays were run with the aim of using the methylation profiles (n=986 in total) for sarcoma subtype classification (Paper: Lyskjær et al, 2021, DNA methylation-based profiling of bone and soft tissue tumours: a validation study of the ‘DKFZ sarcoma Classifier’ ). 500ng of DNA from fresh frozen (FT) or formalin-fixed paraffin-embedded (FFPE) tumour samples were bisulfite converted using the Zymo EZ DNA methylation Gold kit (Zymo Research Corp. Irvine, USA) before hybridisation to the Infinium HumanMethylation450 or EPIC beadchip arrays (Illumina, San Diego, CA) by UCL Genomics. All bisulfite-converted FFPE samples were restored with the Infinium FFPE DNA Restore kit (Illumina).
2021-05-01 | E-MTAB-9875 | biostudies-arrayexpress
Project description:Background: Epigenome-wide association studies (EWAS) have been widely applied to identify methylation CpG sites associated with human disease. To date, the Infinium Methylation EPIC array (EPIC) is commonly used for high-throughput DNA methylation profiling. However, the EPIC array covers only 30% of the human methylome. Methylation Capture bisulfite sequencing (MC-seq) captures target regions of methylome and has advantages of extensive coverage in the methylome at an affordable price. Methods: Epigenome-wide DNA methylation in four peripheral blood mononuclear cell samples was profiled by using SureSelectXT Methyl-Seq for MC-seq and EPIC platforms separately. CpG site-based reproducibility of MC-seq was assessed with DNA sample inputs ranging in quantity of high (> 1000ng), medium (300-1000ng), and low (150ng-300ng). To compare the performance of MC-seq and the EPIC arrays, we conducted a Pearson correlation and methylation value difference at each CpG site that was detected by both MC-seq and EPIC. We compared the percentage and counts in each CpG island and gene annotation between MC-seq and the EPIC array. Results: After quality control, an average of 3,708,550 CpG sites per sample was detected by MC-seq with DNA quantity >1000ng. Reproducibility of MC-seq detected CpG sites was high with strong correlation estimates for CpG methylation among samples with high, medium, and low DNA inputs (r > 0.96). The EPIC array captured an average of 846,464 CpG sites per sample. Compared with the EPIC array, MC-seq detected more CpGs in coding regions and CpG islands. Among the 472,540 CpG sites captured by both platforms, methylation of a majority of CpG sites was highly correlated in the same sample (r: 0.98~0.99). However, methylation for a small proportion of CpGs (N=235) differed significantly between the two platforms, with differences in beta values of greater than 0.5. Conclusions: Our results show that MC-seq is an efficient and reliable platform for methylome profiling with a broader coverage of the methylome than the array-based platform. Although methylation measurements in majority of CpGs are highly correlated, a number of CpG sites show large discrepancy between the two platforms, which warrants further investigation and needs cautious interpretation.
2020-06-11 | GSE152245 | GEO
Project description:EPIC-based DNA methylation analysis of glioblastoma stem cells.
| PRJNA675826 | ENA
Project description:DNA methylation analysis in malignant melanoma clinical samples [EPIC array]
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Project description:DNA methylation from Grady Trauma Project Parental and childhood exposure to trauma increases an individual's lifetime risk for psychiatric and stress-related disorders. This study evaluates DNA methylation in saliva from children, with the goal of identifying associations between peripheral DNA methylation and psychiatric symptoms.
2019-10-02 | GSE138279 | GEO
Project description:Genome-wide DNA methylation profiling using the Illumina EPIC 850k DNA methylation BeadChip array on 8 pools of human genomic DNA from whole blood for 190 individuals age matched at 4 time points; ~4, ~28, ~63, & ~78 years.
2021-02-10 | GSE166503 | GEO