Dynamic, IPSC-derived Hepatic Tissue Tri-Culture System for the Evaluation of Liver Physiology in vitro

This repository is related to the research article entitled "Dynamic, IPSC-derived Hepatic Tissue Tri-Culture System for the Evaluation of Liver Physiology in vitro" by Benedikt Scheidecker et al 2024 Biofabrication 16 025037. DOI 10.1088/1758-5090/ad30c5.

The dataset contains raw RNA sequencing data (FASTQ files generated by paired-end Illumina sequencing of nanoCAGE and Chromium Single Cell 3' Gene Expression libraries) and processed nanoCAGE data files (demultiplexed FASTQ files and sequence alignments in the BED12 file format) produced by the CAGEscan Nextflow pipeline (please see https://gitlab.com/mcfrith/cagescan-pipeline and https://github.com/oist/plessy_CAGEscan_Nextflow for usage details). The nanoCAGE gene expression table (nanoCAGE_exp_table_genes_hg38.csv) was created from BED12 files using the "CAGEr" software package available from Bioconductor. Single cell sequencing data were processed with the dedicated Cell Ranger pipeline available from 10x Genomics.