Identification of the dedifferentiation trajectory of the cells without Arid1a using single cell RNA-seq

ABSTRACT: The primary mouse hepatocytes were isolated from the liver tissue Arid1af/f mouse. To immortalize mouse primary hepatocytes, the isolated cells were first infected with lentivirus expressing simian virus 40 large-T protein (SV40LT), and then cultured until proliferated cell colonies appear. Cells were further transformed with lentivirus expressing HrasV12D to generate a cell line called AB17, which were cultured in DMEM supplemented with 10% FBS and 100 µg/ml penicillin-streptomycin in a humidified incubator at 37℃ with 5% CO2.To get insight into trajectory of dedifferentiation induced by Arid1a loss, we performed single-cell RNA sequencing (scRNA-seq) on FACS-sorted GFP+ AB17 cells using Fluidigm C1 platform, and obtained the scRNA-seq data from 76 cells with Arid1a knockout induced by Ad-Cre and 73 cells infected with Ad-GFP as control. Significantly, these AB17 cells with or without Arid1a were classified to the two distinct clusters based on their scRNA-seq data via the unsupervised clustering with SC3 software and the dimensionality reduction analysis using t-distributed stochastic neighbor embedding (tSNE) visualization, where the major Ad-Cre infected AB17 cells were assembled into cluster 1 while the majority of AB17 cells with empty Ad-GFP as a control belonged to cluster 2. These data suggest that Arid1a loss obviously dysregulated the gene expression pattern, as represented by the top ten differentially expressed genes between these two clusters.

ORGANISM(S): Mus musculus

PROVIDER: GSE140924 | GEO | 2023/07/23

REPOSITORIES: GEO