2.3. Agilent LncRNA chip sequencing

Total RNA was extracted from all cell lines used in this study with TRIzol total RNA isolation reagent (Life Technologies). The Agilent Human LncRNA Microarray 2018 version (4 *180k, Design ID: 085630) was used for chip sequencing and data analysis of HeLa cell samples. In the experimental part, total RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific), and RNA integrity was assessed by an Agilent Bioanalyzer 2100 (Agilent Technologies). After passing the RNA quality inspection, the chip was hybridized and eluted. The original image was obtained by scanning. In the data analysis part, feature extraction software (version 10.7.1.1, Agilent Technologies) was used to process the raw images to extract raw data. Then, quantile normalization and subsequent processing were performed. The normalized data were filtered and at least one set of 100% of the probes marked "P" in each sample used for comparison was retained for further analysis. Finally, the RefSeq IDs of all lncRNAs were extracted from the normalized data table resulting in 137,270 unique lncRNAs.