/DevRetinaST

Spatiotemporal transcriptome atlas of the developing human retina

Primary LanguageRMIT LicenseMIT

Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development

Code and data related to our manuscript "Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development".

Figure 1 - Overview

Main software requirements

  • R 4.3.1
  • Seurat 4.3.0
  • Cell2location 0.1.0
  • OpenCV 4.9.0
  • WGCNA 1.71
  • clusterProfiler 4.10.0
  • COMMOT 0.0.3
  • CellPhoneDB 4.0.0
  • SPARK 1.1.1
  • SCRIPro 1.1.30
  • SpaceRanger 2.1.1

Code

Code for analysis and visualization is avaiable as Rscripts.

Anyone can reproduce results in the manuscript in order based on the file prefix.

Data

  • Raw data: the spatial transcriptome data generated in this study of the human embryonic retina has been deposited at the Genome Sequence Archive for Human (GSA-Human) under the accession number HRA006282.
  • H&E staining: the staining images related to the raw data are avaiable at Staining.

Citation

Zhang et al. (2024) Spatiotemporally resolved transcriptomics reveals the cellular dynamics of human retinal development.