Identification and quantification of gene isoforms during the differentiation of human embryonic stem cells into pharyngeal endoderm and primordial germ cell-like cells

Long-read RNA-seq is now widely applied for gene isoform identification and efforts to long-read RNA-seq for gene isoform quantification are emerging. We develop a software named miniQuant to quantify gene isoforms using long reads alone or in combination with short reads. We demonstrate the utility of miniQuant by its application in uncovering the expression dynamics of gene isoforms during the differentiation of human embryonic stem cells (ESC) into pharyngeal endoderm (PE) and primordial germ cell-like cells (PGC). Overall design: Using the in vitro differentiation systems we have recently developed, we generate definitive endoderm (DE) and pharyngeal endoderm (PE) (as described in our previous paper: DOI: https://doi.org/10.1101/2022.06.26.497457), and primordial germ cell-like cells (PGC) (as described in our previous paper: PMID: 37709760) from human embryonic stem cells (H1-hESC cell line), respectively. We generate long-read RNA-seq data using Oxford Nanopore Technologies (ONT) PCR-cDNA sequencing (cDNA-ONT) and direct RNA sequencing (dRNA-ONT) protocols with one replicate, as well as short-read RNA-seq data using Illumina with three replicates. We identify and quantify gene isoforms in ESC, PE and PGC samples.