The Nephgen scExplorer

The single-cell explorer "scExplorer" is a searchable database to visualize gene expression from RNA-sequencing.

Its intended use is to make datasets generated within the NephGen Initiative (CRC 1453) accessible and searchable, for all researchers within the initiative and to thereby promote scientific collaboration and progress. It allows for downloading of plots, as well as lists of marker genes.
Upon publication the datasets will also be publicly accessible via the scExplorer.

For demonstration, it currently contains data from two published single-cell RNA-seq experiments of human kidney:

• Wu et al:

  Data from 4525 nuclei. Kidney tissue from a single human individual.

  Wu H, Uchimura K, Donnelly EL, Kirita Y, Morris SA, Humphreys BD. Comparative Analysis and Refinement of Human PSC-Derived Kidney Organoid Differentiation with Single-Cell Transcriptomics.
  Cell Stem Cell. 2018;23(6):869-881.e8. doi:10.1016/j.stem.2018.10.010

• Lake et al:

  Data from 17659 nuclei. Kidney tissue from 15 different human individuals.

  Lake BB, Chen S, Hoshi M, et al. A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys.
  Nature Communications. 2019 Jun;10(1):2832. doi:10.1038/s41467-019-10861-2

• Bi et al:

  Data from 34326 cancer and immune cells from 8 RCC patients with ICB treatment (5 patients) or without any systemic treatment (3 patients).

  Kevin Bi, Meng Xiao He, Ziad Bakouny et al. Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma.
  Cancer Cell. Volume 39, Issue 5, 2021, Pages 649-661.e5 doi:10.1016/j.ccell.2021.02.015

Please give it a try by loading a dataset and searching for your genes of interest!




Further References

• Hillje et al:

  The scExplorer application is based upon the "Cerebro" single-cell analysis tool by Roman Hillje.

  Hillje R, Pelicci PG, Luzi L. Cerebro: interactive visualization of scRNA-seq data.
  Bioinformatics. 2020;36(7):2311-2313. doi:10.1093/bioinformatics/btz877




Contact

For questions and feedback, you may contact: oleg.borisov@uniklinik-freiburg.de or stefan.haug@uniklinik-freiburg.de .