Entrain_example_brain_dataset
Description
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
Files
ligand_target_matrix.csv
Files
(18.9 GB)
| Name | Size | Download all |
|---|---|---|
|
md5:5849368845c03f50322a022a462eb6f8
|
347.7 MB | Preview Download |
|
md5:e1f098fd38573bf568b9274082a9ae34
|
83.1 MB | Download |
|
md5:dc0297b2b362166662e5dc6cb652809a
|
10.9 kB | Download |
|
md5:66f92f303795332fc46e9ebe159b62f6
|
4.6 GB | Download |
|
md5:a8595bdf05763ce1f8aeda17817cb119
|
552.9 MB | Download |
|
md5:12f24fb6159e1e24f668cc31ca79979b
|
233.4 MB | Download |
|
md5:f379ee1f3f75d4cabc10cd21c0fbb742
|
4.6 GB | Download |
|
md5:65bb8d4ae8cfe4223a077c439e34f311
|
8.3 GB | Preview Download |
|
md5:9862accd1a0cefb5fc2240a7299ebbdc
|
112.6 MB | Download |
|
md5:06221b9c04f465e59c9da4732df856da
|
40.8 MB | Download |