Transcriptome analysis reveals the mechanism of pyroptosis-related genes in septic cardiomyopathy

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials & Methods

Data source

Differential expression analysis

Functional and pathway enrichment analysis

Expression pattern of the differentially expressed PRGs in SC

Related biological process of differentially expressed PRGs

Prediction of PRG-related miRNAs, transcription factors, and targeted therapeutic drugs

Further validation of differentially expressed PRGs in external datasets

Cell culture and treatment

Cell viability assay

Hoechst 33342 and propidium iodide (PI) staining

siRNA knockdown of SOD2 in AC16 cells

Real-time quantitative polymerase chain reaction

Results

Identification of DEGs and key pathways in SC

Expression pattern of the differentially expressed PRGs in SC

Related biological process of candidate diagnostic biomarkers

Prediction of PRG-related miRNAs, transcription factors, and targeted therapeutic drugs

Further validation of differentially expressed PRGs in external datasets GSE53007 and GSE142615

Cell viability and pyroptosis detection in H9C2 cells

qRT-PCR verification of PRGs in LPS-induced H9C2 and AC16 myocardial cell damage model

Cell viability and pyroptosis detection in SOD2 knocked-down AC16 cells

Discussion

Conclusions

Supplemental Information

Pyroptosis-related genes obtained from previous studies

DOI: 10.7717/peerj.16214/supp-1

The primer sequence information of qPCR experiment

DOI: 10.7717/peerj.16214/supp-2

Information of the DEGs in GSE79962

DOI: 10.7717/peerj.16214/supp-3

The raw data of qPCR

DOI: 10.7717/peerj.16214/supp-4

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Haoyan Zhu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Jiahe Wu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, and approved the final draft.

Chenze Li analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Ziyue Zeng analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Tianwen He analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Xin Liu analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Qiongxin Wang analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Xiaorong Hu conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Zhibing Lu conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Huanhuan Cai conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The data is available at NCBI GEO: GSE79962, GSE53007, GSE142615.

Funding

This study was supported by a grant from the National Natural Science Foundation of China (No. 82070425, Zhibing Lu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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