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We downloaded the target sequences of probes (HG U133 plus 2) from Affymetrix official website ( ), and mapped the target sequence to the lncRNA sequences downloaded from ENSEMBL ( ) with bowtie1 software ( -bio.sourceforge.net/index.shtml) [19]. This mapping step allows no mismatch between Affymetrix probe target sequences and lncRNA reference sequences, and the only probes matched to the forward sequences (parameter -norc) were used for further analysis (strand-specific). Probes matched more than one lncRNAs were discarded. For lncRNAs matched multiple probes, the mean expression value was calculated and took as the expression level of corresponding lncRNAs. At last, 3505 lncRNA were used for further analysis. 59ce067264

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