Four pairs of preretinal membranes were collected for circular RNA expression profiling. RNA high-throughput sequencing was conducted by Cloud-Seq Biotech (Shanghai, China) using total RNA. Initially, the rRNAs were removed with the NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA). RNA libraries were constructed following the manufacturer's instructions, utilizing the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., Ipswich, MA, USA). Quality control and quantification of libraries were performed using the BioAnalyzer 2100 system (Agilent Technologies, Inc., Santa Clara, CA, USA). The libraries were then sequenced on an Illumina Novaseq instrument with 150 base pair (bp) paired-end reads.
Paired-end reads were obtained from the Illumina NovaSeq 6000 sequencer and subjected to quality control with a Q30 threshold. Subsequently, the reads underwent 3' adaptor-trimming and removal of low-quality reads using Cutadapt (version 1.9.3). The high-quality reads were aligned to the reference genome/transcriptome using STAR (version 2.5.1b), and circular RNAs were detected using DCC (version 0.4.4). Data normalization was performed with edgeR (version 3.16.5). Differentially expressed circRNAs (DEcircRNAs) were identified through a t-test between the two groups. CircRNAs exhibiting fold changes (FCs) ≥ 2.0 and an adjusted P value (false discovery rate [FDR]) ≤ 0.15 were considered differentially expressed. Subsequently, functional enrichment analysis, including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, were conducted on the differentially expressed circRNA-associated genes. Significant GO terms and KEGG pathways were identified through the utilization of Fisher's exact test, accompanied by FDR correction applied to the P values. Statistical significance was considered for P values below 0.05. The circRNA-miRNA interactions were predicted using widely used target prediction software. The proprietary software, built upon Targetscan, was utilized to obtain putative miRNA binding sites and target mRNAs. Finally, a regulatory network was generated by Cytoscape (version 3.6.1), revealing the top five putative miRNAs that could bind to the circRNAs.