Computational protocol: HuoXueJieDu Formula Alleviates Diabetic Retinopathy in Rats by Inhibiting SOCS3-STAT3 and TIMP1-A2M Pathways

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Protocol publication

[…] Total RNA from the retinas of rats was extracted. The integrity of the RNA was assessed using the Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, California, USA). Only samples with RNA integrity values larger than 7 and 28S/18S ratios larger than 0.7 were considered qualified. Subsequently, 100 ng of RNA was amplified, labelled, and purified according to the manufacturer's instructions. After hybridization, the microarrays were washed and scanned with default settings according to the manufacturer's instructions (Agilent Technologies, USA). Background correction, quantile normalization, and differential expression analyses were performed using the limma package in the R (version 3.2.4) statistical computing environment. In the limma package, linear models were used to assess the differential expression in the designed microarray experiments. Genes with absolute fold change > 1.5, and P value <0.01 were considered differentially expressed genes (DEGs). Subsequently, pathway enrichment analysis was performed using the Ingenuity Pathway Analysis (IPA) tool. P values were calculated using Fisher's exact test, and P values <0.05 were considered significantly enriched in the canonical pathways []. […]

Pipeline specifications

Software tools limma, IPA
Application Gene expression microarray analysis
Organisms Rattus norvegicus
Chemicals Streptozocin