README.md

Thymus_CITE-seq

Single-cell multi-omic analysis of thymocyte development reveals drivers of CD4/CD8 lineage commitment

Zoë Steier, Dominik A. Aylard, Laura L. McIntyre, Isabel Baldwin, Esther Jeong Yoon Kim, Lydia K. Lutes, Can Ergen, Tse-Shun Huang, Ellen A. Robey, Nir Yosef, Aaron Streets

Nature Immunology, 2023. https://doi.org/10.1038/s41590-023-01584-0

This repository contains code for the analysis performed in this manuscript.

Analysis notebooks

• totalVI_AllData/

  • Filtering_thymus111.ipynb Data preparation and filtering prior to running totalVI on the full CITE-seq data set
  • totalVI_thymus111.ipynb Run totalVI on the full data set

• totalVI_PositiveSelection/

  • Filtering_thymus111_posselecting.ipynb Data preparation and filtering prior to running totalVI on the positive selection subset of the data
  • totalVI_thymus111_posselecting.ipynb Run totalVI on the positive selection subset of the data

• Annotation/

  • Annotation.ipynb Annotation of the full data set and the positive selection subset (run alongside the totalVI notebooks)

• Pseudotime/

  • Slingshot_thymus_posselecting_filtered.Rmd Run Slingshot to generate pseudotime (run alongside differential expression notebooks to plot DE results over pseudotime)
  • Pseudotime_plotting.Rmd Plotting of pseudotime results and in silico FACS analysis

• Differential_Expression/

  • totalVI_thymus111_DE_bintime.ipynb Run differential expression tests with totalVI and generate gene clusters
  • DE_analysis.Rmd Analyze differential expression results and perform trancription factor enrichment analysis

• Multidimensional_Flow/

  • Multidimensional_Flow.ipynb Multidimensional flow analysis

• Vision/

  • Vision_AllData.Rmd Run Vision to generate session for interactive exploration of the full CITE-seq data set
  • Vision_PositiveSelection.Rmd Run Vision to generate session for interactive exploration of the positive selection subset of the data

Data

• The CITE-seq data generated in this manuscript are accessible through GEO: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE186078.

• The anndata objects and pseudotime metadata are accessible through zenodo: https://zenodo.org/doi/10.5281/zenodo.8102049

• The thymus CITE-seq data set can be explored interactively with Vision:

  • Positive selection subset: http://s133.cs.berkeley.edu:9001/Results.html
  • Full data set: http://s133.cs.berkeley.edu:9002/Results.html