A subset of the primate neural differentiation scRNA-seq dataset in an SCE format. The data was collected during the early neural differentiation of human, gorilla and cynomolgus macaque iPS cells with 3 human, 2 gorilla and 4 cynomolgus cell lines (replicates). Using a directed differentiation protocol, cells were differentiated into neural progenitor cells (NPCs) over the course of 9 days, and scRNA-seq data was obtained at six time points (days 0, 1, 3, 5, 7 and 9) during this process. The SCE object contains the raw and log-normalized counts as well as the metadata for 300 genes and 900 cells (100 cells per replicate).
Format
An SCE object with 300 rows, 900 columns, 9 metadata columns and 2 assays.
Metadata columns:
- species
Name of the species.
- replicate
Name of the replicate/cell line.
- day
The day when the cell was collected.
- n_UMIs
Number of UMIs detected.
- n_genes
Number of genes detected.
- perc_mito
Percent of mitochondrial reads.
- sizeFactor
Size factor for scaling normalization, calculated first per replicate using [scran::computeSumFactors] and [scran::quickCluster], then adjusted by [batchelor::multiBatchNorm] to remove systematic differences in covergae across replicates.
- pseudotime
Pseudotime inferred by [SCORPIUS::infer_trajectory].
- cell_type
Cell type labels predicted by [SingleR::classifySingleR] using the embryoid body dataset from Rhodes et al. 2022 as reference.
Assays:
- counts
Raw counts.
- logcounts
Log-normalized counts created by first calculating size factors per replicate using [scran::computeSumFactors] and [scran::quickCluster], then adjusted them to remove systematic differences in covergae across replicates and log-normalizing by [batchelor::multiBatchNorm].