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 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: <strong>Molecular architecture of the developing mouse brain.</strong> <em>Nature </em>2021, <strong>596:</strong>92-96. [2] Abdelaal T, Lelieveldt BPF, Reinders MJT, Mahfouz A: <strong>SIRV: Spatial inference of RNA velocity at the single-cell resolution.</strong> <em>bioRxiv </em>2021<strong>:</strong>2021.2007.2026.453774. [3] Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ: <strong>Generalizing RNA velocity to transient cell states through dynamical modeling.</strong> <em>Nature Biotechnology </em>2020, <strong>38:</strong>1408-1414. [4] Browaeys R, Saelens W, Saeys Y: <strong>NicheNet: modeling intercellular communication by linking ligands to target genes.</strong> <em>Nat Methods </em>2020, <strong>17:</strong>159-162