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Sample GSM4190364 Query DataSets for GSM4190364
Status Public on Jul 23, 2023
Title WL1A3
Sample type SRA
 
Source name AB17
Organism Mus musculus
Characteristics mouse strain: C57BL/6
genotype: Arid1af/f
tissue: liver
Treatment protocol AB17 cells were infected with Ad-GFP or Ad-Cre, respectively. 48 hours after infection, GFP-positive cells were sorted by flow cytometer (BD FACSJazz).
Growth protocol Primary hepatocytes were first isolated from Arid1af/f mice. Isolated cells were then immortalized with SV40LT-expressing lentivirus and then transformed by HrasV12D-expressing lentivirus to generate a cell line named AB17. The AB17 cells were cultured in DMEM medium supplied with 10% fetal bovin serum (FBS) and 100 µg/ml penicillin-streptomycin at 37℃ in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Single cell was captured by the 10-17 µm C1 Single-Cell Auto Prep System (Fluidigm).
Sequencing libraries were constructed using SMARTer (Clontech) whole-transcriptome amplification (WTA) on 73 Ad-GFP infected cells and 76 Ad-Cre infected cells, according to the manufacturer’s instruction. An ERCC Spike-in mix (Ambion) was used as the technical control.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Description infected with Ad-GFP
Data processing Raw sequencing reads were trimmed by Trimmomatic (v0.36) to remove adapters and low quality sequences.
The filtered reads were aligned to the Mus musculus genome GRCm38 UCSC annotated transcripts via Tophat (v2.1.0) with default parameters.
HTSeq (v0.8.0.) was used for transcripts counting for the subsequent statistical analyses were based on negative binomial distribution which requires integer counts. ERCC expressions were used to remove unwanted variation using R Bioconductor package RUVSeq (v1.16.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: counts
 
Submission date Nov 25, 2019
Last update date Jul 23, 2023
Contact name Ze-guang Han
E-mail(s) hanzg@sjtu.edu.cn
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
 
Platform ID GPL21273
Series (2)
GSE140924 Identification of the dedifferentiation trajectory of the cells without Arid1a using single cell RNA-seq
GSE140925 Arid1a in mouse embryonic cells
Relations
BioSample SAMN13382155
SRA SRX7212830

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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