Detecting expressed genes in cell populations at the single-cell level with scGeneXpress

Highlights

• scGeneXpress: a new computational tool designed for identifying expressed genes in single-cell RNA sequencing data.
• scGeneXpress improves the detection of genes expressed at low levels, allowing for a more precise understanding of cellular functions.
• This tool is useful for research in complex tissues, where distinguishing gene expression among different cell types is essential.
• The tool's design is accessible, making it a practical option for researchers without extensive computational expertise.
• This computational tool is relevant for cell engineering, since it enables a more accurate identification of the identity transcription factors of cell populations, which will be used for cellular conversion.

Examining the NEUROG2 lineage and associated gene expression in human cortical organoids

Highlights

• NEUROG1 and NEUROG2 are most highly expressed in basal neural progenitor cells, NEUROG1-derived lineages predominate early and NEUROG2 lineages later.
• NEUROG2 is necessary and sufficient to directly transactivate known target genes (NEUROD1, EOMES, RND2)
• Neurog2 similarly induces Col3a1 & Ppp1r17 in murine P19 cells, consistent with a conservation of NEUROG2 function across mammalian species.