Github repository for "A Stroll Through the Developmental Landscape of Plants"

Folder structure

.
├── LICENSE
├── README.md
├── data.tar.gz
│   ├── Brady2007
│   │   └── brady_markergenes.tsv
│   ├── Denyer2019
│   │   ├── GSE123818_Root_single_cell_wt_datamatrix.csv.gz
│   │   └── supplementary_tab_1.xlsx
│   ├── PlantPhone
│   │   └── LR_pair_ath.RDa
│   └── Shahan2022
│       ├── Root_bulk_arabidopsis_curated.RD
│       └── endo_exp.RD
├── preprocessing
│   ├── 001-PreprocessingLogNormalize.Rmd
│   ├── 002-PreprocessingSctransform.Rmd
│   ├── 003-DimredClustering.Rmd
│   ├── 004-CelltypeAnnotation.Rmd
│   ├── 005-PlotFilteredCells.Rmd
│   └── 006-PloidyTimezone.Rmd
├── project.md
├── report.pdf
├── sessionInfo.txt
└── trajectory_inference
    ├── 007-EpidermalTrajectory.Rmd
    ├── 008-TrajectoryGO.Rmd
    ├── 009-LigandReceptor.Rmd
    └── epidermal_tradeseq.rds

• preprocessing/ contains scripts used for preprocessing the raw gene x cell matrix using Seurat

  • In 001-PreprocessingLogNormalize.Rmd the data was filtered based on QC metrics and log normalized
  • In 002-PreprocessingSctransform.Rmd the data was not filtered and normalized using the regularized negative binomial regression from sctransform
  • In 003-DimredClustering.Rmd the data from 002-PreprocessingSctransform.Rmd was clustered and visualized using UMAP, and we identified cluster-specific marker genes
  • In 004-CelltypeAnnotation.Rmd the clusters were assigned a cell type according to the cluster-specific marker genes and marker genes from Brady 2007 (https://doi.org/10.1126/science.1146265).
  • In 005-PlotFilteredCells.Rmd the cells that were filtered in 001-PreprocessingLogNormalize.Rmd were integrated in the annotated atlas to determine the bias during filtering
  • In 006-PloidyTimezone.Rmd each cell was assigned a ploidy level and developmental zone annotation by correlating its transcriptome with reference profiles (see https://github.com/ohlerlab/COPILOT)

• trajectory_inference/ contains scripts used for trajectory inference on the preprocessed data using Slingshot

  • In 007-EpidermalTrajectory.Rmd we infer developmental trajectories on the subset of epidermal cell types, and perform trajectory differential expression using tradeSeq.
  • In 008-TrajectoryGO.Rmd genes are clustered according to their expression along pseudotime, and we perform GO enrichment analysis on these clusters.
  • In 009-LigandReceptor.Rmd we infer ligand-receptor interactions between the different lineages based on co-expression using PlantPhoneDB.

• data.tar.gz contains all data used during the analysis and sessionInfo.txt contains information on the R package versions.