Collection |

Multi-omics data sharing

'Multi-omics' refers to a family of complex experimental designs where researchers apply more than one molecular profiling technology – capturing, for example, the genome, proteome and metabolome – across a common set of biological samples. These experiments offer a wealth of opportunities for subsequent analyses, but the size of the resulting datasets and the diversity of the study designs makes data sharing inherently challenging. In this collection, we present a series of multi-omics studies where the authors have used innovative means to maximize the accessibility and reusability of their datasets. 

Comment

A special collection on multi-omics data sharing, launched today at Scientific Data, offers to the scientific community a compendium of multi-omics datasets ready for reuse, which showcase the diversity of multi-omics projects and highlights innovative approaches for preprocessing, quality control, hosting and access.

Comment | Open Access | | Scientific Data

In the past decade, there has been a surge in the number of sensitive human genomic and health datasets available to researchers via Data Access Agreements (DAAs) and managed by Data Access Committees (DACs). As this form of sharing increases, so do the challenges of achieving a reasonable level of data protection, particularly in the context of international data sharing. Here, we consider how excessive variation across DAAs can hinder these goals, and suggest a core set of clauses that could prove useful in future attempts to harmonize data governance.

Comment | Open Access | | Scientific Data

Research

Measurement(s) RNA • metabolite • histone_modification • epigenetic status Technology Type(s) RNA sequencing • nuclear magnetic resonance spectroscopy • ChIP-seq Factor Type(s) environmental stress • duration of heat shock • wild type vs Mip6 mutant strain Sample Characteristic - Organism Saccharomyces cerevisiae

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.11836743

Data Descriptor | Open Access | | Scientific Data

Design Type(s) transcription profiling design • molecular interaction analysis objective • metabolic network analysis objective • data integration objective Measurement Type(s) behavioral phenotype • transcription profiling assay • metabolomic assay • physical activity Technology Type(s) electrical potential recording method • RNA sequencing • liquid chromatography-tandem mass spectrometry • Infrared Spectrometry Factor Type(s) experimental condition Sample Characteristic(s) Mus musculus • Cortex • Liver • Blood

Machine-accessible metadata file describing the reported data (ISA-Tab format)

Data Descriptor | Open Access | | Scientific Data

Measurement(s) miRNA • methylation • clinical history • histology • transcription profiling assay • microbiome Technology Type(s) DNA sequencing • clinical monitoring • RNA sequencing • amplicon sequencing • ex vivo photography with digital image analysis • methylation profiling by array Factor Type(s) tumor status Sample Characteristic - Organism Homo sapiens

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9785795

Data Descriptor | Open Access | | Scientific Data

Measurement(s) DNA methylation profiling data • whole genome sequencing assay • bisulfite sequencing assay • transcription profiling assay Technology Type(s) DNA methylation profiling assay • DNA sequencing • RNA sequencing Factor Type(s) age • sex • smoking status Sample Characteristic - Organism Homo sapiens

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9896405

Data Descriptor | Open Access | | Scientific Data

Measurement(s) messenger RNA • miRNA • methylation • deoxyribonuclease activity • assay for transposase-accessible chromatin using sequencing • scRNA • chromatin immunoprecipitation • protein expression profiling • metabolite • metabolite ( http://purl.obolibrary.org/obo/CHEBI_25212 ) Technology Type(s) RNA sequencing • RRBS • DNase-Seq • ATAC-seq • scRNA-seq • scATAC-seq (Microfluidics) • ChIP-seq • mass spectrometry • ultra-performance liquid chromatography-mass spectrometry • gas chromatography-mass spectrometry Factor Type(s) Ikaros level • harvesting time Sample Characteristic - Organism Mus musculus

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9773624

Data Descriptor | Open Access | | Scientific Data

Measurement(s) transcription profiling assay • small RNA sequencing assay • protein profiling assay • hormone measurement • photosynthesis Technology Type(s) RNA sequencing • nanoflow liquid chromatography-tandem mass spectrometry • gas chromatography-mass spectrometry • fluorometer Factor Type(s) days post inoculation Sample Characteristic - Organism Solanum tuberosum

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9891830

Data Descriptor | Open Access | | Scientific Data

Measurement(s) transcription profiling assay • gene mutation • protein profiling assay • neoplastic cell • hematoxylin and eosin stain Technology Type(s) RNA sequencing • DNA sequencing • RPPA protein profiling assay • immunofluorescence microscopy assay • brightfield microscopy Sample Characteristic - Organism Homo sapiens/Mus musculus xenograft

Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.9892316

Data Descriptor | Open Access | | Scientific Data