*3.2. High Throughput Identification*

Multiple methods provide the systematic expression profiling of lncRNAs (Table 1). Although microarrays by predefined probes are not sensitive enough to identify low expression lncRNAs, microarrays have been used to discover novel ncRNAs at the wholegenome level [64]. The lncRNAs' sequence may match the previously built microarrays probe sequences and reannotate the initially protein-coding genes to lncRNAs [65]. A microarray, which hybridizes a selected panel of circRNAs explicitly, can be used to detect the annotated circRNAs expression [66]. For example, Shen et al. used a circRNA microarray and identified 262 upregulated and 291 downregulated circRNAs in ovarian endometriomas [67]. RNA-seq is currently the most widespread approach to discover linear lncRNAs and circRNAs. For example, Bi et al. performed RNA-seq experiments on six pairs of ectopic and eutopic endometria samples with endometriosis and identified 952 differentially expressed lncRNAs [68]. The limitations for RNA-seq data include the limited ability to discern linear and circular lncRNAs of similar sequence and the depth of sequencing required for low read count molecules, such as circRNAs [66,69,70]. Many deep sequencing studies on endometriosis have listed lncRNAs, including circRNAs, within the differentially expressed transcripts, but most of the manuscripts focus on proteincoding genes. Wu et al. identified 8660 upregulated and 651 downregulated lncRNAs [71], and Wang et al. detected 146 upregulated and 148 downregulated circRNAs in ovarian endometriosis by high throughput RNA-seq [72].
