Supplementary collection of preprocessed and analysed data objects for the paper: "Gene-level alignment of single cell trajectories"

Supplementary collection of h5ad data files containing preprocessed and analysed single-cell reference and query datasets discussed in the case studies of the paper:"Gene-level alignment of single cell trajectories" (https://doi.org/10.1101/2023.03.08.531713).

Our artificial thymic organoid raw sequencing data are available from ArrayExpress (E-MTAB-12720).

Below lists the original sources of the literature datasets we downloaded prior to our own preprocessing and trajectory analysis.

Original pan fetal reference data from: Suo, C. et al. (2022) "Mapping the developing human immune system across organs" (https://doi.org/10.1126/science.abo0510), downloaded from https://developmental.cellatlas.io/fetal-immune.

Original healthy/IPF data from: Adams, T. S. et al. (2020), "Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis" (https://doi.org/10.1126/sciadv.aba1983), downloaded from GEO (GSE136831).

We have run our scripts in https://github.com/Teichlab/G2G_notebooks to generate new latent embeddings and infer pseudotime trajectories for the above datasets, and used them to model trajectory alignments with our newly developed framework: ‘Genes2Genes’ https://github.com/Teichlab/Genes2Genes.