Single-cell transcriptomic profiling of a human liver-on-chip model across hypothermic preservation conditions: University of Wisconsin versus hyperbranched polyglycerol solution

ABSTRACT: This dataset contains single-cell RNA sequencing (scRNA-seq) data generated from a multicellular human liver-on-chip model to characterise cell-type-specific transcriptional responses to hypothermic preservation. The organ-on-chip system comprised four cell populations: patient-derived hepatic organoids (PDOs), hepatic stellate cells (HSCs), liver sinusoidal endothelial cells (LSECs), and induced macrophages. Chips were subjected to 24 hours of static cold storage at 6°C using either the clinical standard University of Wisconsin (UW) solution or an experimental hyperbranched polyglycerol (HPG)-based formulation, followed by a 2-hour normothermic reperfusion (rewarming) period. Single-cell transcriptomes were profiled across five conditions: pre-preservation baseline, UW preservation, HPG preservation, post-UW rewarming, and post-HPG rewarming. After quality control, over 20,000 cells were retained for downstream analysis. Dimensionality reduction and unsupervised clustering resolved the four expected cell populations, confirmed by canonical marker expression. Exploratory differential expression analysis identified candidate solution-associated transcriptional differences, including comparatively higher expression of stress, inflammatory, and mitochondrially-encoded transcripts (IFI27, SAA1, HMOX1, MT-ND5) in UW-preserved PDOs. Ligand-receptor inference suggested differential activation of chemokine-mediated intercellular communication axes (CXCL1, CCL20) under UW versus HPG conditions. These findings are hypothesis-generating and require independent biological replication and functional validation. Libraries were prepared using the DNBelab C Series High-throughput Single-cell RNA Library Preparation Set (MGI Tech) and sequenced on the DNBSEQ-G400 platform (paired-end; Read 1: 30 bp, Read 2: 100 bp). Raw reads were aligned to the human GRCh38 reference genome. Downstream analysis was performed using Scanpy v1.11.

INSTRUMENT(S): N/A, DNBSEQ-G400, DNBelab C Series High-throughput Single-cell RNA Library Preparation Set V3.0 (MGI Tech), DNBelab C-TaiM droplet generator (MGI Tech), Avatarget 12-well dual-chamber organ-on-chip system; AvatarFlow Organ Chip Flow Initiation Controller System (Avatarget Co., Ltd., Suzhou, China)

ORGANISM(S): Homo sapiens

SUBMITTER: Joseph Mugaanyi 

PROVIDER: E-MTAB-16925 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress