GSE211949
RNAseq analysis of PM2.5 treated mouse cardiomyocyte cell line
We report the gene expression profile in mouse cardiomyocyte cell line after treatment of PM2.5. Overall design: HL-1 cells were treated with 0.01 and 100 µg/mL PM2.5 for 12 h and then lysed. Total RNA was isolated using QIAzol® (Qiagen, Valencia, CA, USA). Total RNA concentration was quantified using Quant-IT RiboGreen (Invitrogen, Waltham, MA, USA). The integrity of total RNA was determined using TapeStation RNA screentape (Agilent Technologies, Atlanta, GA, USA), and samples with RNA integrity numbers higher than 7 were used for library generation. A library was generated with 1 µg of total RNA from each sample using the Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA, USA). First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen). Second-strand cDNA was synthesized using DNA polymerase I, RNase H, and dUTP. The cDNA samples were processed via end repair by adding a single “A” base and ligating the adapters. The library samples were analyzed using Illumina NovaSeq (Illumina Inc.). Raw reads from the sequencer were preprocessed to eliminate low-quality and adapter sequences before analysis, and the processed reads were aligned to the Mus musculus (mm10) genome using HISAT v2.1.0. Transcript assembly and abundance estimations were performed using StringTie. The aligned reads were assembled, and gene abundance was determined using StringTie v2.1.3b.