Study
Vitamin C boosts DNA demethylation in TET2 germline mutation carriers
| Study ID | Alternative Stable ID | Type |
|---|---|---|
| EGAS00001006916 | Other |
Study Description
We recently identified a family with lymphoma predisposition where a heterozygous truncating germline mutation in TET2 segregated with nodular lymphocyte predominant Hodgkin lymphoma. In a clinical trial of one year, we investigated the effects of oral 1 g/day vitamin C supplementation on DNA methylation by analyzing genome-wide DNA methylation and gene expression patterns from the family members.
Study Datasets 14 datasets.
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
| Dataset ID | Description | Technology | Samples |
|---|---|---|---|
| EGAD00001010009 |
Fasq-files from 3 unaffected TET2 mutation carriers, 2 mutation carriers diagnosed with lymphoma and 3 family members without TET2 mutation. Time series data collected from 0, 6 and 12 months after daily dose of 1g vitamin C.
|
Illumina NovaSeq 6000 | 24 |
| EGAD00010002410 |
Average methylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types using nanopolish. Data from 8 individuals.
|
Oxford Nanopore | 1 |
| EGAD00010002411 |
Average hypermethylation on transcription factor binding sites based on nanopolish calls; only positions showing higher methylation than sample’s average methylation at enhancers were included when defining the average methylation level. Data from 6 individuals at different time points.
|
Oxford Nanopore | 1 |
| EGAD00010002412 |
Average genome-wide methylation levels per sample at different time points using nanopolish calls. Data from 8 individuals.
|
Oxford Nanopore | 1 |
| EGAD00010002413 |
Average methylation levels based on nanopolish calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.
|
Oxford Nanopore | 1 |
| EGAD00010002414 |
Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics chromatin state annotations using different cell types. Data from 8 individuals at different time points.
|
Oxford Nanopore | 1 |
| EGAD00010002415 |
Average hydroxymethylation difference 12 months vs 0 months at Roadmap Epigenomics chromatin state annotations from different cell types. Data from 8 individuals.
|
Oxford Nanopore | 1 |
| EGAD00010002416 |
Proportion of hyper- and hypomethylated positions at Roadmap annotations. Data from 8 individuals.
|
Oxford Nanopore | 1 |
| EGAD00010002417 |
Average hydroxymethylation levels based on megalodon calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.
|
Oxford Nanopore | 1 |
| EGAD00010002418 |
CpG hydroxymethylation. Software: minimap2 v.2.16; Megalodon.
|
Oxford Nanopore | 24 |
| EGAD00010002419 |
Average genome-wide hydroxymethylation levels per sample at different time points using megalodon calls. Data from 8 individuals.
|
Oxford Nanopore | 1 |
| EGAD00010002420 |
CpG methylation. Software: minimap2 v2.16;Nanopolish.
|
Oxford Nanopore | 24 |
| EGAD00010002421 |
Average hydroxymethylation levels on transcription factor binding sites obtained from ENCODE (ChIP-sequencing of GM12878 lymphoblastoid cell line). Data from 6 individuals at different time points.
|
Oxford Nanopore | 1 |
| EGAD00010002422 |
Average methylation levels based on nanopolish calls from Roadmap Epigenomics histone mark annotations using different cell types. Data from 8 individuals at different time points.
|
Oxford Nanopore | 1 |
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