DocTIS makes key molecular datasets and analytical resources available to the scientific community

DocTIS makes key molecular datasets and analytical resources available to the scientific community

As the DocTIS project approaches its conclusion, the consortium is making available a growing collection of molecular datasets, metadata and analytical tools generated throughout six and a half years of research into immune-mediated inflammatory diseases (IMIDs).

These resources represent one of the most comprehensive molecular and computational collections developed within the project, supporting future research on disease mechanisms, treatment response and precision medicine approaches across rheumatoid arthritis, psoriatic arthritis, psoriasis, ulcerative colitis, Crohn’s disease and systemic lupus erythematosus.

In line with the FAIR (Findable, Accessible, Interoperable and Reusable) data principles adopted throughout the project, DocTIS has deposited datasets and analytical resources in public and controlled-access repositories to facilitate transparency, reproducibility and long-term reuse by the scientific community.

The resources have been generated through the collaborative work of the DocTIS consortium, coordinated by the Vall d’Hebron Research Institute, VHIR (Sara Marsal), and involving Cardiff University (Ernest Choy), the University of Verona (Giampiero Girolomoni), Charité – Universitätsmedizin Berlin (Britta Siegmund), the Institut d’Investigacions Biomèdiques August Pi i Sunyer, IDIBAPS (Pere Santamaria), the Centro Nacional de Análisis Genómico, CNAG (Holger Heyn), IMIDomics Inc. (Manuel Lopez-Figueroa), HudsonAlpha Institute for Biotechnology (Richard M. Myers), Linköping University (Mikael Benson), Karolinska Institutet (Mikael Benson) and Zabala Innovation.

Publicly available resources

1- Preprocessed scRNA-sequencing data and metadata for psoriatic arthritis (PsA) patients treated with anti-IL17 therapy

This dataset contains preprocessed single-cell RNA sequencing (scRNA-seq) data and associated metadata from PsA patients classified as responders or non-responders to anti-IL17 treatment at baseline, together with healthy controls.

2- Preprocessed scRNA-sequencing data and metadata for psoriatic arthritis (PsA) patients treated with anti-TNF therapy

This dataset contains preprocessed scRNA-seq data and metadata from PsA patients classified as responders or non-responders to anti-TNF treatment at baseline, together with healthy controls.

3- Preprocessed scRNA-sequencing data and metadata for all IMIDs at baseline and healthy controls

This resource provides harmonised and preprocessed scRNA-seq data from patients across all IMIDs included in DocTIS, together with healthy controls, enabling cross-disease analyses of immune-cell states and inflammatory mechanisms.

4- Code repository for the paper “Interpretable Inflammation Landscape of Circulating Immune Cells”

The repository contains the complete analytical workflows and code used to generate the results presented in the publication, facilitating reproducibility and reuse.

Resources Awaiting Release Following Publication:

5- Raw scRNA-sequencing data and metadata for all IMIDs at baseline and healthy controls

This dataset contains the raw single-cell transcriptomic data and associated metadata generated across all IMIDs included in the project.

The dataset has been submitted to EGA but has not yet been released. Following release, access will be provided through EGA under controlled-access procedures.

6- Raw scRNA-sequencing data and metadata for all IMIDs at follow-up

This resource contains longitudinal scRNA-seq profiles and metadata generated during patient follow-up across all IMIDs included in the project.

The dataset has been uploaded to the repository but has not yet been formally submitted for release. Submission is planned following acceptance of the associated publications (Martínez-Mateu et al. under revision, and Guillén et al. on preparation), currently expected by the end of 2026. Once submitted, access will be available through EGA under controlled-access procedures upon request.

7- Raw bulk RNA-Seq data and metadata for all IMIDs at baseline and follow-up

This dataset contains raw bulk transcriptomic sequencing data and associated metadata generated from patients across all IMIDs, covering both baseline and follow-up time points.

The dataset has been uploaded to the repository but has not yet been formally submitted for release. Submission is expected following acceptance of the associated publication (Martínez-Mateu et al. under revision), currently anticipated by the end of 2026. Once submitted, access will be provided through EGA under controlled-access procedures.

8- Preprocessed bulk RNA-Seq and additional scRNA-seq datasets

This resource includes preprocessed bulk RNA-seq data for all IMIDs at baseline and follow-up, healthy controls, and scRNA-seq data generated from rheumatoid arthritis donors at baseline and follow-up, and healthy donors.

  • Repository: Zenodo
  • Contact person: Sara Marsal (VHIR)
  • Status: Data uploaded.

The dataset has been uploaded and will be released following acceptance of the associated publication (Martínez-Mateu et al. under revision), currently expected by the end of 2026. Once released, the data will be available under request.

9- Code repository supporting the combinatorial therapy analyses

This repository contains the analytical code used in the combinatorial therapy study described in the manuscript by Martínez-Mateu et al., currently under review.

  • Repository: GitHub
  • Contact person: Sergio Martínez (IMIDomics)
  • Status: Code uploaded.

The code has already been uploaded and will be publicly released once the associated publication has been accepted.

Summary of DocTIS data and code resources

ResourceRepositoryStatusContact person
Preprocessed scRNA-seq data and metadata from PsA patients treated with anti-IL17 therapyFigshareAvailableSamuel Schäfer (Linköping University)
Preprocessed scRNA-seq data and metadata from PsA patients treated with anti-TNF therapyFigshareAvailableSamuel Schäfer (Linköping University)
Harmonised preprocessed scRNA-seq data from all IMIDs and healthy controlsZenodoAvailableHolger Heyn (CNAG)
Analytical code for Interpretable inflammation landscape of circulating immune cellsGitHubAvailableHolger Heyn (CNAG)
Raw scRNA-seq data and metadata from all IMIDs at baseline and healthy controlsEuropean Genome-Phenome Archive (EGA)Submitted, pending publicationSara Marsal (VHIR)
Raw scRNA-seq data and metadata from all IMIDs at follow-upEuropean Genome-Phenome Archive (EGA)Uploaded, pending publicationSara Marsal (VHIR)
Raw bulk RNA-seq data and metadata from all IMIDs at baseline and follow-upEuropean Genome-Phenome Archive (EGA)Uploaded, pending publicationSara Marsal (VHIR)
Preprocessed bulk RNA-seq and additional scRNA-seq datasetsZenodoUploaded, pending publicationSara Marsal (VHIR)
Code repository supporting combinatorial therapy analysesGitHubUploaded, pending publicationSergio Martínez (IMIDomics)

Supporting future research in IMIDs

The datasets generated within DocTIS combine single-cell and bulk transcriptomic information, clinical metadata and computational workflows across multiple immune-mediated inflammatory diseases. Together, they provide a valuable resource for researchers interested in disease heterogeneity, treatment response, biomarker discovery and systems medicine approaches.

By making these resources available through recognised public and controlled-access repositories, the DocTIS consortium aims to maximise the long-term scientific impact of the project and support future advances in precision medicine for patients living with IMIDs.

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The DoCTIS project has received funding from the European Union’s H2020 research and innovation program under grant agreement 848028.