This website contains the script for the scRNAseq analysis described in "Temporal patterning of the central nervous system by a shared transcription factor code" by Sagner et al, 2020.
For analysis of spinal cord scRNAseq data, the m_neural.rds file from Delile et al. 2019 was used. The file was generated as described in https://github.com/juliendelile/MouseSpinalCordAtlas.
For analysis of the temporal TFs in the fore-, mid- and hindbrain, please download the dev_all.loom file (app. 19 GB) from Manno et al. 2020 from http://mousebrain.org/downloads.html.
For comparison of temporal TF expression between in-vivo and in-vitro, RNAseq data from Rayon et al. 2020 was used. The file GSE140748_expression_matrix.mouse.abundance.tsv can be obtained from the GEO database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE140748).
For analysis of the temporal TFs in the retina, please download 10X scRNAseq data of the developing retina (count matrix, cellular phenotype data and feature data) from https://github.com/gofflab/developing_mouse_retina_scRNASeq (Clark et al. 2019).
All downloaded files must be placed into the 'input' folder.
| Figure 1 | Figure 2 | Figure 3 |
|---|---|---|
 |
 |
 |
| Figure 4 | Figure 5 | Figure 6 |
|---|---|---|
 |
 |
 |
| Figure 7 | Figure S1 | Figure S2 |
|---|---|---|
 |
 |
 |
| Figure S3 | Figure S4 | Figure S5 |
|---|---|---|
 |
 |
 |
| Figure S6 |
|---|
 |