MASH-CDHFD 0，4，8，12 month-Liver-scRNA-seq Raw Data

Description

Single-cell RNA sequencing was performed on hepatic tissues from both healthy and MASH mice using the 10x Genomics Chromium platform. Sequencing libraries were processed with CellRanger (v4.0.5) for demultiplexing, read alignment to the GRCm38 reference genome, and initial feature-barcode matrix generation. Subsequent processing and quality control were conducted in R (v4.0.5) using the Seurat package (v5.0.4). Low-quality cells were filtered out based on the following criteria: nFeature_RNA between 300 and 7000, nCount_RNA > 1000 (excluding the top 3% of cells with highest UMI counts), mitochondrial gene percentage (mt_percent) < 10%, and hemoglobin gene percentage (HB_percent) < 3%.

Steps to reproduce

Animal groups: Liver samples were collected from mice fed a normal diet (ND) for 12 months, and mice fed a choline‑deficient high‑fat diet (CDHFD) for 4, 8, and 12 months (n = 3–5 per group). Single‑cell suspension: The left lateral liver lobe was immediately processed using the gentleMACS Octo Dissociator and Liver Dissociation Kit (Miltenyi Biotec). After enzymatic and mechanical dissociation, the suspension was filtered through a 70 µm strainer. Hepatocytes were removed by two rounds of low‑speed centrifugation (30 × g, 3 min, 4°C). Non‑parenchymal cells were collected by centrifugation (300 × g, 5 min, 4°C), and red blood cells were lysed with ACK buffer. Quality control: Viability and cell concentration were assessed by trypan blue exclusion. Only samples with viability ≥85% and no visible clumps were used. Single‑cell library preparation & sequencing: Single‑cell libraries were constructed using the Chromium Single Cell 3′ Reagent Kit v3.1 (10x Genomics) targeting 10,000 cells per sample. cDNA amplification and library preparation were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform (paired‑end, 28+90 cycles) to a depth of ≥50,000 reads per cell.

Institutions

• Southeast University

  Jiangsu, Nanjing

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