Discovery of regulators for early steps of endosymbiosis in the soft coral Xenia sp.

Introduction

This repository contains the code and analyses associated with a RNAi study of Xenia sp. presented in the following manuscript:

Minjie Hu, Yun Bai, Xiaobin Zheng, Yixian Zheng (2022) # Discovery of regulators for early steps of endosymbiosis in the soft coral Xenia sp.

Raw data for scRNA-seq are accessible at SRA (Bioproject: PRJNA869069)

Selected/final R analysis objects are available from figshare

Description of files in the repository

R Markdown documents with analysis code.

01CreateSeuratObject.Rmd

• Filter data and create Seurat object for each scRNA library

02LabelTransfer_DoubletFinder.Rmd

• Annotate each cluster according to previous non-regeneration scRNA-data which can be download here. The potential doublets are predicted by DoubletFinder.

03SymbioticTrajectory.Rmd

• Predict the endosymbiotic cell trajectory by Monocle.

04NMFAnalysis.Rmd

• Identify other potential endosymbiosis initiation regulators by NMF.

alga_counting

• Folder containing alga counting script