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bioRxiv:10.1101/2023.02.15.528008 zenodo:10.5281/zenodo.7586958

A Single-cell Perturbation Landscape of Colonic Stem Cell Polarisation

This repository contains Python and R scripts used to generate the figures presented in Qin & Cardoso Rodriguez et. al., A Functional Single-cell Landscape of Colonic Stem Cell Polarisation.

Subsampled versions of some objects are already provided within this repository to facilitate running the notebooks. Otherwise, full datasets exceeding GitHub's file size limit are generally archived in Zenodo, with some available upon request.

Overview

An overview of all the samples generated in this study can be found here, while the folders in this repository are organised by figures.

More specifically:

  • /Figure1_S1 - scRNA-seq - data integration, cell-type-specific analysis, and epithelia focus analysis (incl. clustering, gene signature analysis, differential abundance analysis, entropy analysis, and RNA velocity analysis)

    • IntegrationDR_epifibmac.ipynb: Figure 1B.
    • emdPCA_DE_Epithelia.ipynb: Figure 1C, Figure S1B.
    • emdPCA_DE_Fibroblasts.ipynb: Figure 1C, Figure S1C.
    • emdPCA_DE_Mcrophages.ipynb: Figure 1C, Figure S1D.
    • Main_INTepi.ipynb: Figure 1D-I, Figure S2E.
    • Velocity.ipynb: Figure 1E, Figure S1H-I, Figure S4J-K.
    • fib-signatures.ipynb: Figure S1B.
    • cellchat_cd34-focus.ipynb: Figure S1C.

  • /Figure2_S2 - scRNA-seq - gene signature correlation analysis and integrative analysis with published human data.

    • Signatures.ipynb: Figure 2.
    • HumanReferenceMapping.ipynb: Figure S2A-B, F-H.
    • CMS.ipynb: Figure S2C-D.

  • /Figure3-4_S3-S4 - Mass cytometry (MC) - 'WENR Permutation'.

    • Notebooks split by experiment.
      • /WENR Permutation: Figures 3 & 4, S3 & S4
      • /WNT-EGF Competition: Figure S4C-F.
      • /Ligand Time-course: Figure S4H-I.

  • /Figure5_S5 - scRNA-seq & MC - cell-cell communication analysis, i.e., CellChat analysis & 'CellChat Follow-up'.

    • Notebooks split by experiment.
      • CCommunications.ipynb: scRNA-seq analysis for Figure 5A, Figure 5B, Figure S5A-C, Figure S4G.
      • CMS_CellChat.ipynb: Figure S5D.
      • /CellChat Follow-up: MC analysis for Figure 5D, Figure S5D-H.

  • /Figure6_S6 - MC - Cue-signal-response array, i.e., 'Signal Perturbation'.

    • Notebooks for Figure 6 and Figure S6.

  • /Figure7_S7 - Single-cell valley-ridge (VR) landscape.

Data Availability

  • Raw scRNA-seq data and BioSample metadata have been deposited at Sequence Read Archive (SRA).
  • Raw and processed MC data are available as a Community Cytobank project.
  • Aligned scRNA-seq count matrices, spliced/unspliced RNA count matrices, integrated Seurat objects, integrated MC dataframes, and Houdini project files can be accessed at Zenodo.