Single-cell transcriptomics

Curated Single-Cell RNA-Seq Data

GENEVESTIGATOR® now enables the analysis of deeply curated single-cell RNA-Seq (scRNA-Seq) data from public repositories using its user-friendly visualization tools. Its unique collections of high quality and deeply curated data enable researchers to understand molecular mechanisms of development and disease, and to uncover cellular heterogeneity in normal and diseased tissue. The consistent processing, curation, clustering, cell type identification and harmonization of studies within compendia allow the user to save time and resources and to focus on addressing exciting questions spanning different therapeutic areas.

Curated compendia

Single-cell RNA-Seq studies in GENEVESTIGATOR® are available as extra data subscriptions for chosen focus areas. Currently, data are available for the following areas, each containing baseline seminal studies and more specific studies:

  1. Cardiovascular System
  2. Digestive and Endocrine Systems
  3. Immune System
  4. Nervous System
  5. Oncology
  6. Reproductive and Renal Systems
  7. Respiratory System
  8. Various Systems (currently with data from osteoarthritis, dermatology and others)

To get a more detailed overview of single-cell studies in these areas or in another area of interest, please write to For an overview of all scRNA-Seq offerings, including curation and scouting services, see here.


Curated studies


Cell types


Million cells



Data resolution

scRNA-Seq data are available in GENEVESTIGATOR® at two levels of resolution:

  1. Single-cell level: Data from Smart-Seq libraries are featured as 1 sample = 1 cell.

  2. Aggregate level: Data from droplet-based libraries are featured as 1 sample = 1 aggregate, where an aggregate is a group of cells from the same biosample that have shared attributes, e.g. cell type and cell state. Detailed information on the composition of each aggregate is available in the tooltip.

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Explore two free data sets

With the 2020 autumn update, all users with a valid GENEVESTIGATOR® license get full access to two public scRNA-Seq data sets: MM-01243 (multiple sclerosis study on a single-cell level) and HS-03428 (COVID-19 study on an aggregate level). For a brief introduction on where to find single-cell studies in GENEVESTIGATOR® and what types of visualizations are available, see the following video tutorial:

See also example analyses on these two datasets:

  1. Example visualizations for GSE113973 / MM-01243, a mouse Smart-Seq study
  2. Example visualizations for GSE145926 / HS-03428, a human 10x study

7 days Free trial

To access all deeply curated scRNA-Seq studies in GENEVESTIGATOR®, create a new account or login to your existing account and activate your free trial.