Data collection and preprocessing

The transcriptome expression profile data related to SCI were searched in the NCBI GEO [17] in the database, with the keywords of “spinal cord injury.” The criteria for screening the datasets were as follows: (1) the dataset must be the same species (human, rat, mouse, etc.); (2) the tissues used for study must be uniform tissues (spinal column, blood, spinal fluid, etc.); (3) the data set must had before-and-after damage controls, and each state samples must have duplicates. After screening, two datasets meeting the requirements were included in the analysis: GSE45006 (GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array) and GSE20907 (GPL6247 [Ragene-1_0-ST] Affymetrix Rat Gene 1.0 ST Array [transcript (Gene) version]). GSE45006 contains four spinal tissue samples of 2 weeks after injury and 4 control samples, and GSE20907 contains two spinal tissue samples of 2 weeks after injury and 4 control samples.

We downloaded the original data with format of CEL, and performed original CEL format data conversion, missing value supplement (median method), and data normalization (MAS method and quantiles method) using the R3.6.1 oligo version 1.41.1 [18].

The detail platform annotation information, including probe, gene symbol, and RNA types, was downloaded from Ensembl genome browser 96, and then the detection probes downloaded from the two datasets were reannotated to obtain the expression levels corresponding to lncRNA, miRNA, and mRNA.

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