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Series GSE140924 Query DataSets for GSE140924
Status Public on Jul 23, 2023
Title Identification of the dedifferentiation trajectory of the cells without Arid1a using single cell RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Overall design 48h after infection with Ad-GFP and Ad-Cre, AB17 cells were sorted to get GFP positive cells. Single cell was captured, reverse-transcribed and amplified on Fluidigm C1 platform. The next generation sequencing was performed by Nextera XT DNA library prep kit (Illumina), followed by sequencing on Illumina X Ten platform using a 150 bp paired-end sequencing strategy. An ERCC Spike-in mix (Ambion) was used as the technical control.
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Contributor(s) Han Z, Wang L
Citation(s) 35964817
Submission date Nov 25, 2019
Last update date Jul 24, 2023
Contact name Ze-guang Han
Organization name Shanghai Jiao Tong University
Department Shanghai Center for Systems Biomedicine
Street address 800 Dongchuan Road
City Shanghai
ZIP/Postal code 200240
Country China
Platforms (1)
GPL21273 HiSeq X Ten (Mus musculus)
Samples (149)
GSM4190361 WL1A1
GSM4190362 WL1A10
GSM4190363 WL1A2
This SubSeries is part of SuperSeries:
GSE140925 Arid1a in mouse embryonic cells
BioProject PRJNA591558
SRA SRP233170

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Supplementary file Size Download File type/resource
GSE140924_GeneAndERCC_rawData.txt.gz 2.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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