Published December 19, 2022 | Version v1.0.0
Software Open

Code for the analysis of scRNA-seq data from spinal cord ependymal cells of young and aged mice

Creators

  • 1. Division of Molecular, Cell and Developmental Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
  • 2. Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
  • 3. Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
  • 4. Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK

Description

The adult spinal cord stem cell potential resides within the ependymal cell population and declines with age. Ependymal cells are, however, heterogeneous and the biological diversity this represents and how it changes with age remain unknown. This repository contains the code used to analyse single-cell RNA sequencing data of spinal cord ependymal cells from adult and aged mice that led us to uncover the profiles of all known ependymal cell subtypes and new immature and mature cell states. The R scripts are numbered based on which figure the analyses relate to.

The preprint of the study can be found at: https://www.biorxiv.org/content/10.1101/2022.03.07.483249v1

Raw sequencing data, raw count matrices, and processed data have been deposited at ArrayExpress under accession numbers E-MTAB-11561 (10x Genomics) and E-MTAB-11563 (Smart-seq2).

Notes

This project was supported by the Wellcome Trust (Wellcome Investigator award WT102817AIA to KGS) and a Wings for Life grant to K.G.S. This project and A.R.A. were also supported by the European Union's Horizon 2020 Marie Skłodowska-Curie grant agreement No. 753812. A.R.A was also supported by the Wellcome ISSF COVID-19 Research Momentum fund (119293). G.A.S. was supported by Wings for Life. C.P.P was supported by the MRC (MC_UU_00007/15). A.P.M. was supported by the Chan Zuckerberg Biohub. E.L.-B. and J.F. were supported by the Swedish Research Council, Knut and Alice Wallenbergs Stiftelse and the Swedish Cancer Foundation. The confocal microscope used for imaging was purchased with support from Wellcome Trust Multi-User Equipment grant (WT101468).

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Additional details

Related works

Is supplement to
https://github.com/aidarodrigo/ependymal_cell/tree/v1.0.0 (URL)

Funding

European Commission
ECtomics – Dissecting spinal cord ependymal cell heterogeneity by single-cell transcriptomics 753812

References

  • Rodrigo Albors et al. (2022). Code for the analysis of scRNA-seq data related to bioRxiv 10.1101/2022.03.07.483249v1