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Dataset results
53 results for “DNA methylation, cell type”
Data and Code for "Cell Type-specific Genome Scans of DNA Methylation Diversity Indicate an Important Role for Transposable Elements"
<p>This is a release of the gitlab repository "meta-methylome" (https://gitlab.com/okartal/meta-methylome.git) that, in addition to the code, also contains the resulting genomic data.</p> <p>Extract the directory on the command line using</p> <pre><code class="language-bash">$ tar -xhzvf meta-methylome.tar.gz</code></pre> <p>to preserve the symbolic links.</p>
Multi-cell type deconvolution using a probabilistic model for single-molecule DNA methylation haplotypes
<p>Files required to run deconvolution with CelFIE-ISH and Epistate, in U250 regions from Loyfer et al. 2023, in both "pat" and "epiread" formats. </p>
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
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Unique cell-type specific patterns of DNA methylation in the root meristem (MethylC-seq)
GEO Series GSE79708. Arabidopsis thaliana. 9 samples. Type: Methylation profiling by high throughput sequencing.
Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Mouse Reference Cell-type MCC-seq]
GEO Series GSE200185. Mus musculus. 8 samples. Type: Methylation profiling by high throughput sequencing.
Unique cell-type specific patterns of DNA methylation in the root meristem (RNA-seq)
GEO Series GSE79709. Arabidopsis thaliana. 6 samples. Type: Expression profiling by high throughput sequencing.
Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type MCC-seq]
GEO Series GSE200093. Homo sapiens. 12 samples. Type: Methylation profiling by high throughput sequencing.
DNA methylation profiles in pneumonia patients reflect changes in cell types and pneumonia severity
GEO Series GSE192702. Homo sapiens. 127 samples. Type: Methylation profiling by high throughput sequencing.
A Cell Type Enrichment Analysis Tool for Brain DNA Methylation Data (CEAM) [BDR]
GEO Series GSE306226. Homo sapiens. 80 samples. Type: Methylation profiling by array.
Circulating, cell-free methylated DNA reveals cellular sources of allograft injury after liver transplant (LTR reference cell type)
GEO Series GSE262274. Homo sapiens. 14 samples. Type: Methylation profiling by high throughput sequencing.
DNA methylation profiles of Purified Blood Cell types
GEO Series GSE166844. Homo sapiens. 217 samples. Type: Methylation profiling by array.
Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex
GEO Series GSE289184. Homo sapiens. 87 samples. Type: Methylation profiling by array.
Genome-wide DNA methylation analysis of different cell types
GEO Series GSE74877. Homo sapiens. 24 samples. Type: Methylation profiling by genome tiling array.
Multi-cell type deconvolution using a probabilistic model of single-molecule DNA methylation haplotypes
GEO Series GSE239605. Homo sapiens. 205 samples. Type: Methylation profiling by high throughput sequencing.
Circulating cell-free, methylated DNA reveals tissue-specific, cellular damage from radiation treatment [Human Reference Cell-type RNA-seq]
GEO Series GSE200095. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
DNA methylation profiles of four immune cell types from MS patients and healthy controls
GEO Series GSE173787. Homo sapiens. 133 samples. Type: Methylation profiling by high throughput sequencing.
Cell Type-Specific DNA Methylation at Intragenic CpG Islands in the Immune System (gene expression data)
GEO Series GSE25578. Mus musculus. 18 samples. Type: Expression profiling by array.
Role of DNA methylation in FOXA1 cell type-specific recruitment to chromatin
GEO Series GSE21513. Homo sapiens. 13 samples. Type: Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array.
Differential DNA methylation and changing cell type proportions as fibrotic stage progresses in NAFLD
GEO Series GSE180474. Homo sapiens. 341 samples. Type: Methylation profiling by array.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.