Differential Gene Expression Analysis

Total RNA from the renal cortex tissue was extracted following the TRIzole method (Invitrogen, Carlsbad, CA). Subsequently, the quantity and integrity of the RNA was measured using the NanoDrop 8,000 (Thermo Scientific) and the Agilent Bioanalyzer 2,100 (Agilent Technologies), respectively. Refer to the Affymetrix manual for cRNA related experiments (Campus IFOM IEO, Italy). Samples were hybridized onto a Human Clariom D gene chip (Affymetrix, Santa Clara, California). The R statistical software pre-processed imported raw CEL files, and the Robust Multichip Average algorithm under the oligo package was used to normalize the data. The raw data were investigated using the transcriptome analysis console software (Applied Biosystems, Foster City, USA). A significant (p-value < 0.05) absolute fold change in gene expression of ≥ 1.5 indicated differentially expressed genes (DEGs). The R software (heatmap V1.0.12 and ggplot2 V3.3.6) was used to generate heatmaps and volcano plots of significant DEGs (Tian et al., 2021 (link)).

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Wang Y., Liu Y., Chen S., Li F., Wu Y., Xie X., Zhang N., Zeng C., Bai L., Dai M., Zhang L, & Wang X. (2023). The protective mechanism of Dehydromiltirone in diabetic kidney disease is revealed through network pharmacology and experimental validation. Frontiers in Pharmacology, 14, 1201296.

Publication 2023

TRIzole NanoDrop 8,000 Agilent Bioanalyzer 2,100 transcriptome analysis console software

Crna Gene chip Gene expression Genes Human Oligo Renal cortex Tissue Transcriptome analysis

Corresponding Organization : University of Electronic Science and Technology of China

Other organizations : Suzhou Municipal Hospital, Nanjing Medical University, Sir Run Run Shaw Hospital, Zhejiang University, Huashan Hospital, Fudan University

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Variable analysis

independent variables

Tissue extraction method (TRIzole method)

dependent variables

Quantity of RNA
Integrity of RNA
Gene expression (differentially expressed genes)

control variables

Renal cortex tissue

controls

No positive or negative controls were explicitly mentioned in the provided information.

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