Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm

Published: 16 October 2023| Version 1 | DOI: 10.17632/s25d8y9pvz.1


All single cell sequencing datasets, R scripts and installation instructions. The following instructions allows you to download R and Rstudio to view any gene expression from the single cell datasets. Download R: Visit the Comprehensive R Archive Network (CRAN) website, the official source for R: Choose a CRAN mirror location near you. Select the mirror that's geographically closest to your location for faster download speeds. Click on the appropriate link for your operating system (Windows, macOS, or Linux). Follow the installation instructions for your specific operating system. Typically, this involves downloading the installer and running it. Install R: Run the downloaded installer. Follow the on-screen instructions, including choosing installation options if prompted. Once the installation is complete, you will have R installed on your computer. Download RStudio: Visit the RStudio download page: Scroll down to the "RStudio Desktop" section. Click on the appropriate link for your operating system (Windows, macOS, or Linux). Download the installer for RStudio Desktop. Install RStudio: Run the downloaded RStudio installer. Follow the on-screen instructions to complete the installation. Once you've completed these steps, you'll have both R and RStudio installed on your computer. You can then launch RStudio, and it will automatically detect your R installation and provide an integrated development environment for working with R. You are then able to open up of the four R markdown files (.Rmd) and load in the datasets from the Rds_object folders in order to view the datasets. Descriptions on the R scripts and Rds objects uploaded below: Three folders containing R codes and the input to the codes as Rds object format. Navigate into the folder and open the rmd or r script files with R studio and follow the instruction inside to run codes. All script should be able to run with minor edit to the data path customed to each user. All scripts inside each folders should be able to run without requiring the outputs of other scripts. To visualize gene expression of single cell seq dataset as shown in the paper, use folder "1. UMAP_Gene_Viewer". To reproduce the UMAP and sequencing results from annotated matrix files, use folder "2. UMAP, differential analysis and cell trajectory pipeline". To integrate multiple datasets, use folder 3.


Steps to reproduce

Refer to method section of the paper for experimental details regarding single-cell sequencing from early drosophila embryos.


California Institute of Technology


Developmental Biology, Drosophila, Single-Cell RNA Sequencing