This is the code and data repository of the paper "Fate and State Transitions during Human Blood Vessel Organoid Development". The preprinted version of paper is available at bioRxiv. The paper has been accepted in Cell.
The raw data of the scRNA-seq and scMultiome data sets generated in this paper are available in ArrayExpress:
- Time course profiling of BVO and transplanted BVO: E-MTAB-14807
- Perturbation experiments: E-MTAB-14839
All the Seurat objects will be available in Zenodo with the following DOI: 10.5281/zenodo.14002044
In this repository, the codes are organized by their related figures.
- fig1_timecourse: to analyze the time course scRNA-seq data of the in vitro culture BVOs
- fig2_transplanted: to analyze the scRNA-seq data of transplanted BVOs
- fig3_multiome: to analyze the scMultiome data of the in vitro BVOs
- fig4_cropseq_MECOM: to analyze the CROP-seq data and scRNA-seq data of MECOM-KO experiments
- fig5_VEGF_Notch: to analyze the scRNA-seq of BVO with NEGF and Notch manipulation
- fig6_BBB_like: to analyze scRNA-seq of experiments attempting to steer BVO to blood-brain-barrier identity
- fig7_disease: to analyze scRNA-seq data of disease modeling with BVO