Supplementary collection of preprocessed and analysed data objects for the paper: "Gene-level alignment of single cell trajectories"
Creators
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1.
Wellcome Sanger Institute
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2.
University of Cambridge
- 3. Princess Máxima Center for Pediatric Oncology
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4.
Seoul National University
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5.
Korea Advanced Institute of Science and Technology
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6.
Columbia University
Description
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.
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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.
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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.
Files
Files
(7.0 GB)
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md5:d5b6df7b8355b81bc2c0800ff6683c28
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md5:79d5fb88f600d47c2e25357d674a1c98
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md5:02abacf010e6c04b4d6b3939aaf70987
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md5:6bd90b6b049af79b06f481fd79eb3ea4
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md5:ee48d414eee4efb7df4d24192e3aef67
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md5:88f0e22a2208a1ed8296588a1558dc13
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md5:588b90a89b218efcc034856ed78eee0d
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Additional details
Related works
- Is supplement to
- https://github.com/Teichlab/G2G_notebooks (URL)
References
- Suo, C. et al. Mapping the developing human immune system across organs. Science (2022)
- Adams, T. S. et al. Single-cell RNA-seq reveals ectopic and aberrant lung-resident cell populations in idiopathic pulmonary fibrosis. Science Advances (2020)