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80 results for “cfDNA”
cfDNA UniFlow Testfiles
<p>This repository contains files used for testing the correct execution of cfDNA UniFlow prior to productive use. It contains small bam and fastQ files based on IC17 from Snyder et al. 2016 (Cell): <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1833242">GSM1833242</a> / <a href="https://www.ncbi.nlm.nih.gov/sra?term=SRX1120780">SRX1120780</a>.</p> <p>A step-by-step documentation of how these files were generated from the original IC17 sample is included in "create_testsample.md".</p> <p>Original paper:</p> <p>Snyder MW, Kircher M, Hill AJ, Daza RM, Shendure J. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin. Cell. 2016; doi: 10.1016/j.cell.2015.11.050.</p>
sequenced cfDNA samples, extracted DoC for TSSs (HK + PAU) and TFBSs (LYL1 and GRHL2)
<p>File contains CSV files which store depth of coverage values (cfDNA fragment's central 60 bp if length > 60 bp; entire fragment otherwise) extracted from 4 samples (sample BAM files deposited at the European Genome Phenome Archive, accession: <span> </span><a href="https://ega-archive.org/studies/EGAS00001006963">EGAS00001006963</a><span><span>) before and after correction of sample specific GC sequence content bias (GC bias) by GCparagon software using a custom Pysam implementation. The Pysam implementation can read alignment tags for DoC computation which is required for the signal after bias correction.</span></span></p> <p><span><span>Extracted loci are top 10k reported transcription factor binding sites for LYL1 and GRHL2 as well as transcription start sites of housekeeping genes (HK genes) and unexpressed genes as assessed from the Protein atlas (PAU genes).<br> Pysam implementation by Kapidzic Faruk can be found here: </span></span><a href="https://github.com/Faruk-K/pysam">https://github.com/Faruk-K/pysam</a></p> <p>Linked to the <a href="https://github.com/BGSpiegl/GCparagon/tree/including_EGAS00001006963_results-DEV">GCparagon tool code repository</a> which is available on GitHub.</p> <p>For details see publication which is linked to the EGA dataset and the GitHub repository. (not published at moment of submission to Zenodo)</p>
Fragmentomic analysis of cfDNA from LFS
<p>Processed data files for reproducing figures from the publication "Cell-free DNA from germline <em>TP53</em> mutation carriers reflect cancer-like fragmentation patterns"</p>
A novel CRISPR screen identifies mediators of cfDNA release
Open the record for dataset details and reuse information.
Development of a cfDNA 5mC/5hmC-based Biomarker Panel to Predict Targeted Therapy Efficacy in mCRC
ClinicalTrials.gov study NCT07224841. IPD Sharing: NO. Countries: 1. Publications: 15.
A Single-center, Prospective Cohort Study on the Differentiation of Benign and Malignant Bile Duct Stenosis Based on Bile and Peripheral Blood cfDNA Methylation Profiles
ClinicalTrials.gov study NCT06115655. IPD Sharing: NO. Countries: 1. Publications: 7.
Analysis of Cell-free DNA (cfDNA) in Men With Elevated PSA Levels
ClinicalTrials.gov study NCT02771769. IPD Sharing: YES. Countries: 1. Publications: 3.
Methylation of cfDNA in Diagnosing and Monitoring Pulmonary Nodule
ClinicalTrials.gov study NCT03989219. IPD Sharing: NO. Countries: 1. Publications: 1.
Characterization & Comparison of Drugable Mutations in Primary and Metastatic Tumors, CTCs and cfDNA in MBCpatients
ClinicalTrials.gov study NCT02626039. IPD Sharing: Not stated. Countries: 1. Publications: 1.
iDentification and vAlidation Model of Liquid biopsY Based cfDNA Methylation and pRotEin biomArKers for Pancreatic Cancer (DAYBREAK Study)
ClinicalTrials.gov study NCT05495685. IPD Sharing: NO. Countries: 1. Publications: 49.
Gastric Cancer Early Detection by Multi-dimensional Analysis of cfDNA
ClinicalTrials.gov study NCT05668910. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Trifecta-Kidney cfDNA-MMDx Study
ClinicalTrials.gov study NCT04239703. IPD Sharing: NO. Countries: 10. Publications: 12.
Trifecta-Heart cfDNA-MMDx Study
ClinicalTrials.gov study NCT04707872. IPD Sharing: NO. Countries: 7. Publications: 5.
Exploring a Breast Cancer Early Screening Model Based on cfDNA
ClinicalTrials.gov study NCT06016790. IPD Sharing: NO. Countries: 1. Publications: 1.
Analysis of cfDNA in Patients With Hepatocarcinoma and Treated by Sorafenib or Regorafenib
ClinicalTrials.gov study NCT03956940. IPD Sharing: NO. Countries: 1. Publications: 15.
Clinical Study of Microchimerism and cfDNA as Biomarkers for Acute Rejection After Organ Transplantation
ClinicalTrials.gov study NCT03255265. IPD Sharing: Not stated. Countries: 1. Publications: 28.
Plasma cfDNA Fragmentomics for Early pNET Detection and Differential Diagnosis of Solid Pancreatic Tumors
ClinicalTrials.gov study NCT05847855. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Oxidative Stress and Circulating Nuclear DNA (cfDNA) in Acute Kidney Injury and Continuous Renal Replacement Therapies.
ClinicalTrials.gov study NCT06646328. IPD Sharing: NO. Countries: 1. Publications: 55.
Auxiliary Diagnosis of Liver Nodules Using cfDNA Whole-genome Signatures
ClinicalTrials.gov study NCT05393102. IPD Sharing: NO. Countries: 1. Publications: 4.
cfDNA 5mC/5hmC Biomarkers to Predict Chemotherapy Response in Metastatic Colorectal Cancer
ClinicalTrials.gov study NCT07224815. IPD Sharing: NO. Countries: 1. Publications: 17.
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
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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.