Entrain_example_brain_dataset
Single-cell RNA sequencing dataset of the developing mouse brain at E10 and E11, produced by [1], and processed by [2]. Data has been subset to E10 and E11 and subsampled to 5% of original cells. RNA Velocity matrix has been run on this dataset, using scvelo [3] workflow. Also att
Single-cell RNA sequencing dataset of the developing mouse brain at E10 and E11, produced by [1], and processed by [2]. Data has been subset to E10 and E11 and subsampled to 5% of original cells.
RNA Velocity matrix has been run on this dataset, using scvelo [3] workflow.
Also attached, for convenience, is the required NicheNet database on intercellular regulation [4].
[1] La Manno G, Siletti K, Furlan A, Gyllborg D, Vinsland E, Mossi Albiach A, Mattsson Langseth C, Khven I, Lederer AR, Dratva LM, et al: Molecular architecture of the developing mouse brain. Nature 2021, 596:92-96.
[2] Abdelaal T, Lelieveldt BPF, Reinders MJT, Mahfouz A: SIRV: Spatial inference of RNA velocity at the single-cell resolution. bioRxiv 2021:2021.2007.2026.453774.
[3] Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ: Generalizing RNA velocity to transient cell states through dynamical modeling. Nature Biotechnology 2020, 38:1408-1414.
[4] Browaeys R, Saelens W, Saeys Y: NicheNet: modeling intercellular communication by linking ligands to target genes. Nat Methods 2020, 17:159-162
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Files are hosted on the source repository. Click download to access the full dataset.