GSE183013 Next Generation Sequencing Facilitates Transcriptomes Quantitative Analysis of siRNA mediated ASGR1 knockdown

Contributors : Ju-Qiong Wang ; Bao-Liang SongSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: The goal of this study is to demonstrate the gene profiles of ASGR1 knock down mediated by siRNA compared with siControl in Huh7 cells.Methods: The Huh7 cells were transfected with small interference RNA (siRNA) targeting scramble (WT) or ASGR1 (AS2) for 8 hours, then cells were refreshed with Dulbecco's Modified Eagle Medium (DMEM) supplemented with 100 units ml-1 penicillin, 100 μg ml-1 streptomycin sulfate, and 10% fetal bovine serum (FBS). After 72 hours, the cells were harvested for RNA isolation and followed by high-throughput sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcriptome with Hisat2(v 2.0.1). qRT–PCR validation was performed using SYBR Green assays.Results: Using an optimized data analysis workflow, we mapped about 45 million sequence reads per sample to the human genome in the WT and AS2 cell lines Hisat2 (v2.0.1). RNA-seq data confirmed stable expression of the known housekeeping genes, and these genes were validated with qRT –PCR. RNA-seq data had a linear relationship with qRT–PCR for more than a goodness of fit (R2) of 0.9. Approximately 4.2% of the transcripts showed significantly differential expression between the WT and AS2 cell lines, with a log2 fold change ≥1.0 and p value

Source: GEO: Gene Expression Omnibus - May 19, 2022 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research