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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2024 |
| Title |
MSA: Scalable DNA methylation BeadChip for human trait screening |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
We designed and introduced a new methylation array concentrating on human trait screening and discovery. The new MSA (Methylation Screening Array) leveraged the massive Infinium platform-based data from epigenome-wide association studies, combined with updated knowledge from the latest single cell and cell type-resolution whole genome methylome profiles, to achieve scalable screening of epigenetics-trait association in an ultra-high sample-throughput. Our design encompassed diverse human trait associations, including those with genetic, biological, and demographical variables, environmental exposures, and common human diseases such as neurodegenerative, genetic, cardiovascular, infectious, and immune diseases. We comprehensively evaluated the reproducibility, accuracy, and capacity of comprehensive cell-type deconvolution in diverse human tissues. Our first data using this platform uncovered dynamic chromatin and tissue contexts of DNA methylations with human trait associations.
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| Overall design |
Cell line (GM12878, K562, LNCaP, HeLa, Raji, MCF7, Jurkat, HCT116 and other Coriell cell lines), and 8 human tissue (skin, pancreas, colon, heart, PBMC, motor cortex, cerebellum, whole blood) and purified cell DNA (CD4+ T cells, CD8+ T cells, total T cell, NK cells, monocytes) and methylation titration control DNA is run on the MSA BeadChip to evaluate MSA reproducibility, accuracy, performance at low input ranges, and capability at capturing biological methylation variation. Cerebellum, motor cortex, colon, pancreas, skin, heart are additionally processed with bACE conversion to obtain 5hmC profiles.
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| Contributor(s) |
Goldberg D, Zhou W |
| Citation(s) |
38826316 |
| Submission date |
Apr 19, 2024 |
| Last update date |
Jun 12, 2024 |
| Contact name |
Wanding Zhou |
| Organization name |
Children's Hospital of Philadelphia
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| Department |
Pathology and Lab Medicine
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| Street address |
3501 Civic Center Blvd
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platforms (1) |
| GPL34394 |
Infinium Methylation Screening Array (MSA) |
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| Samples (420)
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| Relations |
| BioProject |
PRJNA1102411 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE264438_GEOprocessed_matrix_GPL34394.csv.gz |
1.3 Gb |
(ftp)(http) |
CSV |
| GSE264438_GEOsignal_intensity_matrix_GPL34394.csv.gz |
2.1 Gb |
(ftp)(http) |
CSV |
| GSE264438_RAW.tar |
2.2 Gb |
(http)(custom) |
TAR (of IDAT) |
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