Pre-processing of six temporal multi-modal single-cell datasets. The raw and pre-processed data can be downloaded from here (for HC, HO, DR, and MN data) and here (for ZB and AM data).
The preprocessing script for each dataset are provided in the corresponding directory. If you want to re-run the preprocessing, remember to change file path according to your environments.
| ID | Dataset | Species | # RNA Cells | # RNA Timepoints | # ATAC Cells | # ATAC Timepoints | Co-Assay Data | Source |
|---|---|---|---|---|---|---|---|---|
| HC | human cortex | Homo sapiens | 2277 | 10 | 2277 | 10 | Yes | [1] |
| HO | human organoid | Homo sapiens | 10000 | 11 | 10000 | 11 | Yes | [2] |
| DR | drosophila | Drosophila melanogaster | 2738 | 11 | 4246 | 11 | No | [3] |
| MN | mouse neoctex | Mus musculus | 6098 | 3 | 1914 | 3 | No | [4] |
| ZB | zebrahub | Danio rerio | 3692 | 6 | 9456 | 6 | No | [5] |
| AM | amphioxus development | Branchiostoma lanceolatum | 9630 | 6 | 3538 | 6 | No | [6] |
[1] Zhu, K., Bendl, J., Rahman, S., Vicari, J. M., Coleman, C., Clarence, T., ... & Roussos, P. (2023). Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Science Advances, 9(41), eadg3754.
[2] Fleck, J. S., Jansen, S. M. J., Wollny, D., Zenk, F., Seimiya, M., Jain, A., ... & Treutlein, B. (2023). Inferring and perturbing cell fate regulomes in human brain organoids. Nature, 621(7978), 365-372.
[3] Calderon, D., Blecher-Gonen, R., Huang, X., Secchia, S., Kentro, J., Daza, R. M., ... & Shendure, J. (2022). The continuum of Drosophila embryonic development at single-cell resolution. Science, 377(6606), eabn5800.
[4] Yuan, W., Ma, S., Brown, J. R., Kim, K., Murek, V., Trastulla, L., ... & Arlotta, P. (2022). Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex. Nature Neuroscience, 25(8), 1049-1058.
[5] Lange, M., Granados, A., VijayKumar, S., Bragantini, J., Ancheta, S., Kim, Y. J., ... & Royer, L. A. (2024). A multimodal zebrafish developmental atlas reveals the state-transition dynamics of late-vertebrate pluripotent axial progenitors. Cell, 187(23), 6742-6759.
[6] Ma, P., Liu, X., Xu, Z., Liu, H., Ding, X., Huang, Z., ... & Chen, D. (2022). Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution. Cell Reports, 39(12).