{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Joseph Mugaanyi"],"organism":["Homo sapiens"],"software":["N/A","Cell Ranger (10x Genomics); Scanpy v1.11 (Python)","Scanty (v1.11, Python)","DNBC4Tools (MGI Tech)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16925"],"description":["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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - DNA NanoBalls (DNBs) were generated from the indexed libraries and loaded onto patterned nanoarrays for sequencing on the DNBSEQ platform (MGI Tech) using paired-end sequencing chemistry (Read 1: 30 bp; Read 2: 100 bp; Index: 10 bp). Raw sequencing reads were processed using the Cell Ranger pipeline, aligned to the human reference genome GRCh38 to generate gene–barcode count matrices. Sequencing targeted a minimum of ~20,000 high-quality cells across five experimental conditions.","Nucleic Acid Extraction - Single-cell suspensions were processed immediately after dissociation. Cell viability and concentration were assessed prior to library preparation. Single cells were encapsulated into droplets using the DNBelab C Series droplet generation workflow (MGI Tech), which co-encapsulates individual cells with barcoded beads carrying poly-dT primers, enabling per-cell mRNA capture. Following droplet generation, emulsions were broken, and barcoded beads were collected for reverse transcription and cDNA synthesis. No spike-in controls (e.g., ERCC) were added.","Sample Collection - Cells were cultured in a twelve-well dual-chamber organ-on-chip system (Avatarget Co., Ltd., Suzhou, China) for three days at 37°C with 5% CO₂. Chips were randomized into three groups: Baseline (collected on Day 3), 24-hour hypothermic preservation in University of Wisconsin (UW) solution at 6°C, or 24-hour hypothermic preservation in Hyperbranched Polyglycerol (HPG) solution at 6°C. A subset of preservation groups underwent 2-hour normothermic reperfusion (rewarming) prior to collection. Cells were dissociated using Trypsin; organoids were digested with TrypLE for 5–10 minutes, filtered through a 40 µm strainer, and resuspended in cell cryopreservation medium.","Library Construction - Single-cell RNA-seq libraries were constructed using the DNBelab C Series High-throughput Single-cell RNA Library Preparation Set (MGI Tech) following the manufacturer's protocol. Briefly, following reverse transcription and cDNA amplification, indexed sequencing libraries were generated. The library structure consists of a paired-end design: Read 1 (30 bp) encodes cell barcode 1 (positions 1–10 bp), cell barcode 2 (positions 11–20 bp), and a 10 bp UMI (positions 21–30 bp), while Read 2 (100 bp) contains the cDNA transcript sequence. A 10 bp sample index read was also generated for demultiplexing. Library quality and quantity were assessed prior to sequencing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Raw gene–barcode count matrices were processed using Scanpy (v1.11, Python). Quality control filters removed cells with fewer than 300 detected genes or mitochondrial transcript content exceeding 20%. Library-size normalisation was applied by scaling each cell to a total count of 10,000, followed by log1p transformation. Highly variable genes were identified and used for dimensionality reduction via Principal Component Analysis (PCA). Nearest-neighbour graph construction, Leiden clustering, and UMAP visualisation were performed on the PCA embedding. Pseudobulk differential expression, trajectory inference, and ligand-receptor interaction analyses were conducted on the normalised, log-transformed expression matrix."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["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)"],"study_type":["single nucleus RNA sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Joseph Mugaanyi"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell transcriptomic profiling of a human liver-on-chip model across hypothermic preservation conditions: University of Wisconsin versus hyperbranched polyglycerol solution","description":"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.","dates":{"release":"2026-04-17T00:00:00Z","modification":"2026-05-06T12:36:33.119Z","creation":"2026-04-17T11:03:08.261Z"},"accession":"E-MTAB-16925","cross_references":{"ENA":["ERP192292"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009809","EFO_0005518","EFO_0003816","EFO_0004184"]}}