Human ESC Neuronal differentiation

We have developed a neuronal differentiation protocol and performed a multiomics study of  single-cell RNA-seq and ATAC-seq at four time points: From Human Embryonic Stem Cells (Day 0), and Days 7, 13 and 20 of neuronal differentiation. Here we present two webtools where you can explore these datasets.

Human ESC Neuronal differentiation scRNA-seq

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Here we present a searchable interactive web-tool utilising ShinyCell for the scRNA-seq from human ESCs Day 0, and neuronal differentiation time points Day 7, 13 and 20. This allows for exploration of gene expression in individual cells and annotated cell populations during the timeline of the differentiation.

Human ESC Neuronal differentiation scATAC-seq

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We have performed scATAC-seq to explore chromatin accessibility landscapes in the cells in the beginning (ESC, Day 0) and at differentiation endpoint (Day 20). The data has been analyzed using ArchR and is openly available in a web tool based on our in house ShinyArchR.UiO. Take a tour into the epigenetic landscape of these cells and utilize different functionalities to learn more about gene regulation during differentiation.

Citing our work: The multiomics study Samara et al., "A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D" is published in iScience. The original preprint is in bioRxiv.org. The details of hESC differentiation is described in Star Protocols. Code is available in EskelandLab Github. Processed datasets are deposited in NCBI GEO: GSE192858

This data generated at the University of Oslo and is available in these tools under the permissive CC BY 4.0 license.

Published Oct. 19, 2022 2:52 PM - Last modified Sep. 7, 2023 11:15 PM