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433
datasets available to search
ShareScore release 0.9.0
Dataset results
433 results for “WGBS”
cao_esophageal_wgbs_hg19
<p>A HDF5-backed RangedSummarizedExperiment for WGBS Data (hg19 CpG sites) for 10 esophageal cancer tumours and 9 matching normal esophageal samples from the paper 'Cao, Wei, et al. "Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma." <em>Nature communications</em> 11.1 (2020): 3675.'. </p>
mcrpc_wgbs_hg38_chr11
<p>A HDF5-backed RangedSummarizedExperiment for WGBS Data (hg38 CpG sites) for chr11 for 100 castration-resistant prostate cancer metastases from the paper 'Zhao, Shuang G., et al. "The DNA methylation landscape of advanced prostate cancer." <em>Nature genetics</em> 52.8 (2020): 778-789.'. </p>
cpgea_wgbs_hg38
<p>A HDF5-backed RangedSummarizedExperiment for WGBS Data (hg38 CpG sites) for 187 pairs of primary prostate tumours and matching normal prostate samples from the paper 'Li, Jing, et al. "A genomic and epigenomic atlas of prostate cancer in Asian populations." <em>Nature</em> 580.7801 (2020): 93-99.'. </p>
target_rhabdoid_wgbs_hg19 and transcript counts
<p>A HDF5-backed RangedSummarizedExperiment for WGBS Data (hg19 CpG sites) for 69 rhabdoid tumours and RNA-seq transcript counts for 65 of these samples from the paper 'Chun, Hye-Jung E., et al. "Genome-wide profiles of extra-cranial malignant rhabdoid tumors reveal heterogeneity and dysregulated developmental pathways." <i>Cancer cell</i> 29.3 (2016): 394-406.'. </p>
mcrpc_wgbs_normal_samples_hg38
<p> HDF5-backed RangedSummarizedExperiment for WGBS Data (hg38 CpG sites) for 10 normal samples from the paper 'Zhao, Shuang G., et al. "The DNA methylation landscape of advanced prostate cancer." <em>Nature genetics</em> 52.8 (2020): 778-789.'. </p>
tcga_wgbs_meth_rse_chr1
<p>A RangedSummarizedExperiment object for hg38 chromosome 1 methylation data for the samples from the paper "DNA methylation loss in late-replicating domains is linked to mitotic cell division"</p>
Test data for running snakePipes : WGBS workflow
<p><strong>Test files for running snakePipes workflows</strong></p> <p><strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to <a href="https://snakepipes.readthedocs.io/en/latest/">this link</a> for further information on snakePipes.</p> <p>This folder contains test files that can be used to run the WGBS workflow under snakePipes. To test the workflow, follow the following steps : </p> <ul> <li>Download or prepare genome fasta, indices and annotations for the mouse (<strong>GRCm38</strong>) genome.</li> <li>Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`</li> <li>Update <a href="https://snakepipes.readthedocs.io/en/latest/content/running_snakePipes.html#genome-configuration-file">Genome configuration file</a> with path to indices and annotations.</li> <li>Move to this repository and run the example <strong>command.sh</strong></li> </ul>
Test data for running snakePipes : WGBS workflow
<p><strong>Test files for running snakePipes workflows</strong></p> <p><strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to <a href="https://snakepipes.readthedocs.io/en/latest/">this link</a> for further information on snakePipes.</p> <p>This folder contains test files that can be used to run the WGBS workflow under snakePipes. To test the workflow, follow the following steps : </p> <ul> <li>Download or prepare genome fasta, indices and annotations for the mouse (<strong>GRCm38</strong>) genome.</li> <li>Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`</li> <li>Update <a href="https://snakepipes.readthedocs.io/en/latest/content/running_snakePipes.html#genome-configuration-file">Genome configuration file</a> with path to indices and annotations.</li> <li>Move to this repository and run the example <strong>command.sh</strong></li> </ul>
mcrpc_wgbs_hg38
<p>A HDF5-backed RangedSummarizedExperiment for WGBS Data (hg38 CpG sites) for 100 castration-resistant prostate cancer metastases from the paper 'Zhao, Shuang G., et al. "The DNA methylation landscape of advanced prostate cancer." <em>Nature genetics</em> 52.8 (2020): 778-789.'. </p>
WGBS from body of pancreas (ENCSR996BJT)
GEO Series GSE127328. Homo sapiens. 1 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from liver (ENCSR660CKG)
GEO Series GSE82862. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Transient naive reprogramming corrects hiPS cells functionally and epigenetically [WGBS 2]
GEO Series GSE160933. Homo sapiens. 21 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from forebrain (ENCSR019HJV)
GEO Series GSE82355. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from stomach (ENCSR286OOJ)
GEO Series GSE82571. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing [WGBS]
GEO Series GSE128731. Homo sapiens. 41 samples. Type: Methylation profiling by high throughput sequencing.
Comprehensive analyses of partially methylated domains and differentially methylated regions in esophageal cancer reveal both cell-type- and cancer-specific epigenetic regulation [WGBS]
GEO Series GSE210218. Homo sapiens. 2 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from kidney (ENCSR906HLA)
GEO Series GSE83011. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from GM12878 (ENCSR890UQO)
GEO Series GSE86765. Homo sapiens. 2 samples. Type: Methylation profiling by high throughput sequencing.
An epigenetic switch ensures transposon repression upon acute loss of DNA methylation in ES cells (WGBS)
GEO Series GSE71592. Mus musculus. 1 samples. Type: Methylation profiling by high throughput sequencing.
WGBS from embryonic facial prominence (ENCSR735PMJ)
GEO Series GSE82907. Mus musculus. 4 samples. Type: Methylation profiling by high throughput sequencing.
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.