RNA-seq and Data Collection

A circRNA profile was generated from an Illumina Hiseq yielding total RNA from a mixture of primary chondrocytes from five individuals treated with 500 μM of H₂O₂ for five days (H₂O₂-MIX) compared to a mixture of negative control primary chondrocytes from the same five individuals (NC-MIX) as previously reported ⁴¹. The remaining samples were used for quantitative real-time PCR (qRT-PCR) to validate the profile. A | log₂ (fold change) | > 1 and FDR ≤ 0.05 was regarded as significantly different.

The other datasets used in our study were obtained from the following sources: Circbase (http://www.circbase.org/) for annotation of circRNA; TargetScan (http://www.targetscan.org/vert_72/), RNAhybrid ⁴² and RegRNA (http://regrna2.mbc.nctu.edu.tw/) for prediction of target miRNAs of circRNAs; TargetScan, RNA22 (https://cm.jefferson.edu/rna22/), and miRDB (http://mirdb.org/) for forecasting downstream mRNAs of miRNAs. The Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/, GSE 86578, {"type":"entrez-geo","attrs":{"text":"GSM2306261","term_id":"2306261"}}GSM2306261, {"type":"entrez-geo","attrs":{"text":"GSM2306265","term_id":"2306265"}}GSM2306265, {"type":"entrez-geo","attrs":{"text":"GSM2306269","term_id":"2306269"}}GSM2306269, {"type":"entrez-geo","attrs":{"text":"GSM2306268","term_id":"2306268"}}GSM2306268, {"type":"entrez-geo","attrs":{"text":"GSM2306272","term_id":"2306272"}}GSM2306272, and {"type":"entrez-geo","attrs":{"text":"GSM2306264","term_id":"2306264"}}GSM2306264) was used to detect differential mRNA expression induced by pro-inflammatory cytokines. EBI (https://www.ebi.ac.uk/Tools/psa/) was employed for pairwise sequence alignment.