Processed cell cycle-dependent gene expression (scRNA-seq) mESC data

Processed scRNA-seq data for the paper "Cell-cycle dependence of bursty gene expression: insights from fitting mechanistic models to single-cell RNA-seq data". 

This a reprocessed scRNA-seq dataset of mouse embryonic stem cells (mESCs) with inhibited differentiation, originally generated by Riba et al. (2019) using the 10x Genomics Chromium platform, containing spliced and unspliced transcript counts for over 5000 cells and more than 10000 genes. We have reprocessed the original FASTQ data deposited by the authors in the GEO database and reapplied DeepCycle (from Riba et al. (2019)) to extract the transcriptional phase information and associate each cell with a specific cell-cycle phase (G1, S and G2/M). See the manuscript for more details. 

The uploaded .h5ad file is an AnnData object, which contains the spliced and unspliced discrete mRNA transcript count (UMI) matrices for all cells and genes in the mESC population, as well as the cell-specific transcriptional phase and cell-cycle phase information. The dataset is used for the mechanistic model-based inference and analysis presented in the paper.