Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
200
datasets available to search
ShareScore release 0.9.0
Dataset results
200 results for “Methylation array”
Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies
<p>Data corresponding to the paper "Crossreactive probes on Illumina DNA methylation arrays: a large study on ALS shows that a cautionary approach is warranted in interpreting epigenome-wide association studies."<br> <br> Corresponding scripts can be found at: <a href="https://github.com/pjhop/dnamarray_crossreactivity">https://github.com/pjhop/dnamarray_crossreactivity</a><br> All downstream analyses in <a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/c9_analysis.Rmd">c9_analysis.Rmd</a> and in<a href="https://github.com/pjhop/dnamarray_crossreactivity/blob/master/analysis/supplementary_note.Rmd"> supplementary_note.Rmd</a> can be reproduced using the deposited data as follows:</p> <ul> <li>Clone the dnamarray_crossreactivity repository: < git clone https://github.com/pjhop/dnamarray_crossreactivity.git ></li> <li>Download the data ('data.zip') and place it in the 'dnamarray_crossreactivity' folder.</li> <li>Unzip the data.zip folder</li> </ul> <p>Scripts used to generate the data in each subdirectory can be found at:</p> <ul> <li>data/processed/c9_matches/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/c9_matches</a></li> <li>data/output/ewas/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/ewas</a></li> <li>data/output/figs/: empty folder, running 'c9_analysis.Rmd' will save figures here.</li> <li>data/misc/: <a href="https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other">https://github.com/pjhop/dnamarray_crossreactivity/tree/master/analysis/other</a></li> <li>data/extdata: <ul> <li>Zhou <em>et al.</em> annotations (EPIC.hg19.manifest.tsv.gz, HM450.hg19.manifest.pop.tsv.gz, HM450.hg19.manifest.tsv.gz) were downloaded from: <a href="https://zwdzwd.github.io/InfiniumAnnotation">https://zwdzwd.github.io/InfiniumAnnotation</a> (downloaded at 17/09/2020)</li> <li>Naeem <em>et al.</em><em> </em>data (12864_2013_7006_MOESM2_ESM.csv) was downloaded from: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943510/</a></li> <li>Chen <em>et al.</em> data (48639-non-specific-probes-Illumina450k.xlsx) was downloaded from <a href="https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx">https://github.com/Jfortin1/funnorm_repro/blob/master/bad_probes/48639-non-specific-probes-Illumina450k.xlsx</a></li> <li>The anno_450k.txt.gz and anno_EPIC.txt.gz are subsets of the annotation files included in the following package respectively: <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylation450kanno.ilmn12.hg19.html</a> and <a href="https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html">https://bioconductor.org/packages/release/data/annotation/html/IlluminaHumanMethylationEPICanno.ilm10b2.hg19.html</a></li> </ul> </li> <li> data/genome_bs: Scripts used to generate these data can be found at <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R</a> and <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R</a> .</li> <li> data/raw: Individual-level data is available upon access at: <a href="https://ega-archive.org/studies/EGAS00001004587">https://ega-archive.org/studies/EGAS00001004587</a></li> </ul>
Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery
<p>Data Associated with Figures 1 and 2 in Communications Biology Matters Arising: Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery. Original data arising from B. Li et al. <i>Communications Biology</i> <a href="https://doi.org/10.1038/s42003-022-03353-5">https://doi.org/10.1038/s42003-022-03353-5</a> (2022)</p>
Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array]
GEO Series GSE34340. Homo sapiens. 6 samples. Type: Methylation profiling by genome tiling array.
Assessment of DNA methylation patterns related to femur bone morphology in nonhuman primate bone using the 850K array
GEO Series GSE103287. Callithrix jacchus; Macaca mulatta; Homo sapiens; Papio sp.; Chlorocebus aethiops; Pan troglodytes. 58 samples. Type: Methylation profiling by array.
Array-based DNA-methylation analysis in individuals with developmental delay/intellectual disability and normal molecular karyotype
GEO Series GSE64380. Homo sapiens. 100 samples. Type: Methylation profiling by array.
DNA methylation status of myelinating Schwann cells during development and in diabetic neuropathy [Gene Expression Array: GNMT mice]
GEO Series GSE45701. Mus musculus. 4 samples. Type: Expression profiling by array.
DNMT and EZH2 inhibitors synergize for gene activation in hepatocellular carcinoma cells [methylation array]
GEO Series GSE202559. Homo sapiens. 24 samples. Type: Methylation profiling by genome tiling array.
Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2
GEO Series GSE51245. Homo sapiens. 40 samples. Type: Methylation profiling by array.
Multi-omic colon organoid analysis highlight MSH4 as a marker of Lynch syndrome and microsatellite instability [methylation array]
GEO Series GSE210018. Homo sapiens. 58 samples. Type: Methylation profiling by array; Methylation profiling by genome tiling array.
Methylation array of arecoline treated human gingival epithelial cells
GEO Series GSE157246. Homo sapiens. 2 samples. Type: Methylation profiling by genome tiling array.
TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states [DNA methylation array - d10earclips]
GEO Series GSE229030. Mus musculus. 58 samples. Type: Methylation profiling by genome tiling array.
The SEQC2 epigenomics quality control (EpiQC) study [methylation array]
GEO Series GSE230132. Homo sapiens. 30 samples. Type: Methylation profiling by genome tiling array.
Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses [methylation]
GEO Series GSE81788. Homo sapiens. 8 samples. Type: Methylation profiling by array.
Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East Asia [DNA Methylation Array]
GEO Series GSE314841. Homo sapiens. 161 samples. Type: Methylation profiling by genome tiling array.
In vitro methylation studies in multiple human cell types [HumanMethylation850 array]
GEO Series GSE197723. Homo sapiens. 317 samples. Type: Methylation profiling by genome tiling array.
Genome-wide methylation studies in nasal epithelial cells using a custom Asthma&Allergy DNAm array
GEO Series GSE267595. Homo sapiens. 474 samples. Type: Methylation profiling by genome tiling array.
Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify differences in DNA methylation [Array]
GEO Series GSE169218. Mus musculus; Rattus norvegicus; Homo sapiens. 80 samples. Type: Methylation profiling by genome tiling array.
Joint-specific DNA methylation signatures in rheumatoid arthritis [methylation array]
GEO Series GSE80071. Homo sapiens. 24 samples. Type: Methylation profiling by genome tiling array.
DNA demethylating agents represent a therapeutic opportunity for synovial sarcoma [Methylation array]
GEO Series GSE291314. Strix uralensis; Mus musculus. 8 samples. Type: Methylation profiling by array.
DNA methylation and hydroxymethylation assessment through Illumina EPIC array analysis of paired bisulfite and oxidative-bisulfite conversion
GEO Series GSE144129. Homo sapiens. 454 samples. Type: Methylation profiling by genome tiling 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.