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. As of October 2020, data are available for the following areas, each containing baseline seminal studies and more specific studies:

  1. Immune System
  2. Oncology
  3. Nervous System
  4. Digestive and Endocrine Systems
  5. Reproductive and Renal Systems
  6. Various Systems (currently with osteoarthritis data)

To get a more detailed overview of single-cell studies in these areas or in another area of interest, please write to


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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With the 2020 autumn release, two test data sets are available for free to all users: MM-01243 (mouse study on a single-cell level) and HS-03428 (human study on an aggregate level). To explore the data sets, simply use the keyword search of the data selection. See also how GENEVESTIGATOR® can be used to analyze single-cell transcriptomic data:

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

How to get access

To access our deeply curated compendia on GENEVESTIGATOR®, please contact us at For more information about our compendia and curation services, see here.