Transcriptomic Analysis of Murine Cardiac Samples

RNA samples of murine heart tissue were collected from C57BL/6 mice treated with or without DOX and stored with RNAStore solution at 4 °C (#DP408-02, Tiangen Biotech Co., Ltd.). RNA isolation, quality control, library construction, and sequencing were performed by the Beijing Genomics Institute (www.genomics.org.cn, BGI) using the BGISEQ-500 platform. Cleaned reads were then mapped to the GRCm38.P6 reference genome with Bowtie2 (v2.2.5)^{17 (link)}. Transcript abundances were measured with RSEM (v1.2.8)¹⁸. Further bioinformatics analyses were all accomplished in RStudio with R (v3.5.3) and GSEA (v4.0.3) with GSKB (v1.14.0)^{19 –21}. Low count genes were removed by a cut-off at 0.5829 FPKM. Differential expression analyses were performed with limma (R packages v3.38.3) by a cut-off at 1.44-fold-change and P value < 0.05^{22 (link)}. KEGG pathway enrichment was performed with clusterProfiler (v3.10.1)^{23 (link)}. Plots performed with ggplot2 (v3.2.1) and ggpubr (v0.2.4)^{24 ,25}. Heatmap of 50 up-regulated genes and 50 down-regulated genes was plotted with pheatmap (v1.0.12)²⁶. All codes are available from the corresponding author upon request.

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Liu Y., Zeng L., Yang Y., Chen C., Wang D, & Wang H. (2020). Acyl-CoA thioesterase 1 prevents cardiomyocytes from Doxorubicin-induced ferroptosis via shaping the lipid composition. Cell Death & Disease, 11(9), 756.

Publication 2020

RNAStore solution

C57bl mice Down Genes Heart Isolation Library Murine Tissue

Corresponding Organization :

Other organizations : Huazhong University of Science and Technology, Tongji Hospital

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Variable analysis

independent variables

Treatment with or without DOX

dependent variables

Transcript abundances measured with RSEM
Differential gene expression
KEGG pathway enrichment

control variables

C57BL/6 mice
RNA samples of murine heart tissue

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