Fig. 1

Overview of experimental design, modified 10x protocol, FLAMES method, and basic summary statistics. A Summary of the study design, with an overview of the modified 10x protocol and FLAMES data processing pipeline. B UMAP visualization of cells in each sample, cells colored in red are sampled for long-read sequencing. scmixology1 and scmixology2 were integrated and shown together in one plot. All UMAP visualizations are based on short-read data. C The number of nanopore reads generated from each sample, and the percentage of reads that were assigned a cell barcode. D Distribution of UMI counts per cell for Illumina and nanopore data in each sample. E Correlations between gene UMI counts generated from nanopore long-read and Illumina short-read data. F Density scatter plot shows the relationship between transcript-level counts and scATAC-seq read counts around the TSS regions. The horizontal orange line shows the threshold calculated that separates open chromatin from the background. The percentage shows the transcripts that have their TSSs in open chromatin regions