Lineage dynamics of the endosymbiotic cell type in the soft coral Xenia

Introduction

This repository contains the code and analyses associated with a single-cell RNA-seq study of Xenia sp. presented in the following manuscript:

Minjie Hu, Xiaobin Zheng, Chen-Ming Fan, and Yixian Zheng (2020) Lineage dynamics of the endosymbiotic cell type in the soft coral Xenia https://www.nature.com/articles/s41586-020-2385-7

The transcriptome and the genome can be accessed via Carnegie Coral & Marine Organisms

Raw data used for de novo genome assembly, gene prediction and scRNA-seq are accessible at SRA (Bioproject: PRJNA548325)

Selected/final R analysis objects are available from Carnegie Coral & Marine Organisms

Description of files in the repository

R Markdown documents with analysis code (also available as knitted html files).

1_CreateSeuratObject.Rmd

• Filter data and create Seurat object for each scRNA library

2_ClusterAnalysis.Rmd

• Integrate data from non-regeneration samples, initial clustering, and determine markers for each cluster.

3_SymbioticCellIdentification.Rmd

• Compare with FACS transcriptome and identify endosymbiotic cell cluster

4_RNAvelocityAnalysis.Rmd

• RNA velocity analysis for regeneration sample, defining early and late endosymbotic cell

5_MonoclePseudotimeAnalysis.Rmd

• Monocle pseudotime analysis for all endo-symbiotic cells, defining pre-endosymbiotic, transition1, mature, transition2, and post-endosymbiotic states.

Additional files

All data files needed to repeat the analysis can be fetched through following commands:

git clone https://github.com/ciwemb/endosymbiosis
wget -r -np -nH --reject="index.html*" \
        http://cmo.carnegiescience.edu/endosymbiosis/