Find research datasets worth reusing

opencc-by-4.0Mar 2022View details →

Somatic mutations alter the differentiation outcomes of iPSC-derived neurons (Metadata and AnnData/H5AD files)

Data S1: Metadata information for the 828,937 processed cells from the DN dataset: donor identity, cell type annotation, pool identifier, 10x sample, time point and replicate information. Related to STAR Methods: Reanalysis of pooled single-cell data (DA). Data S2-S4: AnnData/H5AD files containing the single-cell gene expression matrices and the metadata for day 11, day 30 and day 52, respectively. The gene expression is normalised and log-transformed, but not scaled. md5 files are also included. Related to STAR Methods:  DE analysis between failed and successful lines. #File names: File-Data S1:     suppData1.RDS File-Data S2:     allpools.scanpy.D11.wMetaClustUmapGraph.exprLogNormNotScaled_notKO.h5ad File-Data S3:     allpools.scanpy.D30.wMetaClustUmapGraph.exprLogNormNotScaled_notKO.h5ad File-Data S4:     allpools.scanpy.D52.wMetaClustUmapGraph.exprLogNormNotScaled_notKO.h5ad

opencc-by-4.0Sep 2022View details →

Common anti-cancer therapies induce somatic mutations in stem cells of healthy tissue

Genome-wide mutation analyses have revealed that specific anti-cancer drugs are highly mutagenic to cancer cells, but the mutational impact of anti-cancer therapies on normal cells is not known. Here, we examine genome-wide somatic mutation patterns in 42 healthy adult stem cells (ASCs) of the colon or the liver from 14 colorectal cancer patients (mean of 3.2 ASC per donor) that received systemic chemotherapy and/or radiotherapy. The platinum-based chemo-drug Oxaliplatin induces on average 535±260 mutations in colon ASC, while 5-FU shows a complete mutagenic absence in most colon ASCs. In contrast with the colon, normal liver ASCs escape mutagenesis from systemic treatment. Radiation results in the accumulation of 50-100 5-10,000bp deletions and structural rearrangements in colon ASCs. Thus, while chemotherapies are highly effective at killing cancer cells, their systemic use also increases the mutational burden of long-lived normal stem cells responsible for tissue renewal thereby increasing the risk for developing second cancers.

openmit-licenseSep 2024View details →

A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology

Source Data and Supplementary Data associated with the paper “A multiscale functional map of somatic mutations in cancer integrating protein structure and network topology” (DOI: https://doi.org/10.1101/2023.03.06.531441).

opencc-by-4.0Jan 2022View details →

Research data supporting article "Somatic mutation rates scale with lifespan across mammals"

Data files supporting analyses described in the article "Somatic mutation rates scale with lifespan across mammals" (Cagan, Baez-Ortega et al., 2022).

opencc-by-4.0Dec 2019View details →

DATA for manuscript entitled "Integrating Transcriptomes and Somatic Mutations to Identify RNA Methylation Regulators as a Prognostic Marker in Hepatocellular Carcinomas"

Raw data of TCGA dataset and 7-meta data.

opencc-by-4.0Jan 2024View details →

A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.

A comparative analysis of somatic mutations occurring at "common" loci and other loci with the TCGA somatic mutation dataset.

opencc-by-4.0Jun 2024View details →

Supplementary videos for the article "Simulation of Somatic Evolution Through the Introduction of Random Mutation to the Rules of Conway's Game of Life"

List of Supplementary Videos:  Supplementary Video 1: Animation of simulation run in the absence of mutation (mutation rate = 0). Supplementary Video 2: Animation of simulation run with mutation rate = 0.01 and mutation magnitude = 1.0. Supplementary Video 3: Animation of simulation run with mutation rate = 0.05 and mutation magnitude = 6.0. Supplementary Video 4: Animation of simulation run with a mutation rate = 0.01 and a mutation magnitude = 5.0. Supplementary Video 5: Animation of simulation run with a mutation rate = 0.05 and a mutation magnitude = 0.5. Supplementary Video 6: Animation of simulation run with a mutation rate = 0.05 and a mutation magnitude = 1.0. Supplementary Video 7: Animation of simulation run with a mutation rate =0.4 and a mutation magnitude = 1.5. Supplementary Video 8: Animation of simulation run with a mutation rate =0.1 and a mutation magnitude = 0.5.

opencc-by-4.0Mar 2019View details →

Simulation data for "Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing"

Simulation data used in analysis of single cell variant calling softwares in manuscript "Conbase:  a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing" Two sets of simulation experiments were performed, one with varying sequencing depth (simulation.tar.gz) and one with a fixed depth at 30 (simulation_fixedDP.tar.gz).

closedIPD-NOFeb 2026View details →

Cutaneous Mastocytosis in Children: Analysis of Somatic and Germline Mutations

ClinicalTrials.gov study NCT02761473. IPD Sharing: NO. Countries: 1. Publications: 4.

restrictedIPD-UNDECIDEDFeb 2026View details →

Evaluation of Somatic Mutation Spectrum as Biomarker for Survival Outcome in Chinese CRC

ClinicalTrials.gov study NCT04228614. IPD Sharing: Not stated. Countries: 1. Publications: 6.

controlledIPD-YESFeb 2026View details →

Autosomal Dominant Polycystic Kidney Disease Somatic Mutation Biorepository

ClinicalTrials.gov study NCT03901521. IPD Sharing: YES. Countries: 1. Publications: 7.