| Filename | Size | Content | Date Modified |
|---|---|---|---|
| gene count (*mtx) | 61GB | open using Matrix::readMM( ) in R or scanpy.read_mtx( ) in Python | 2023-7-30 |
| gene count (*h5ad) | 42GB | open using scanpy.read_h5ad( ) in Python | 2023-7-30 |
| cell meta information | 617MB | keep updated | 2023-7-30 |
| gene expression across timepoints (6 hours) | 926MB | It contains 190 files, each corresponding to a single cell type. Within each file, you'll find 4 columns: gene, day, mean_expression, and pct_cells_expressed_gene. These columns are used to generate the barplot on the "GeneExp" page. | 2024-2-16 |
| gene expression across somite counts (2 hours) | 626MB | It contains 190 files, each corresponding to a single cell type. Within each file, you'll find 4 columns: gene, somite_counts, mean_expression, and pct_cells_expressed_gene. These columns are used to generate the barplot on the "GeneExp" page. | 2024-2-16 |
| gene count exon and intron | 47GB | The exon/intron UMI counts for individual embryos, which are used for RNA-velocity analysis if needed. | 2024-6-24 |
The data generated in this study can be downloaded in raw forms from the NCBI GEO under GSE186069 and GSE228590.
The code used here has been provided from https://github.com/ChengxiangQiu/JAX_code.
To replicate the analysis or generate the figures presented in the manuscript, please follow the scripts provided on the above GitHub page along with the corresponding intermediate datasets provided here.
Please email CX Qiu ( cxqiu@uw.edu ) if any questions!