Supplementary files to the article "Spinal cord RNA-seq data after a baclofen treatment in mice with a spinal cord injury"
Description
A compression spinal cord injury was performed at the T10-T11 level in mice. Injured mice received an IP treatment with baclofen (1m/kg) or the vehicle (control group) once a day for 7 days. At day 7 the spinal cord was collected (0.5 cm and -0.5 cm from the site of injury) and total RNA was extracted for transcriptomic analysis. This supplementary excel files show: 1) Differentially expressed genes between baclofen and control treated spinal cord samples. 2) Enrichment analysis. 3) Grouped enrichment analysis. 4) Transcription factor target enrichment analysis.
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Steps to reproduce
Differential expression (DE) analyses were performed using R v.4.1.1 (https://www.r-project.org/). Gene count data were used to estimate differential gene expression using the Bioconductor package DESeq2 v.3.4. Briefly, size factors were calculated for each sample using the “median of ratios” method and count data was normalized to account for differences in library depth. Next, gene-wise dispersion estimates were fitted to the mean intensity using a parametric model and reduced toward the expected dispersion values. Finally, a negative binomial model was fitted for each gene and the significance of the coefficients was assessed using the Wald test. The Benjamini-Hochberg false discovery rate (FDR) multiple test correction was applied, and genes with FDR < 0.05 were considered differentially expressed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), BioCarta pathways and InterPro domain enrichment analyses were performed using the DAVID bioinformatics resource Functional Annotation tool, using the mouse transcriptome as background. Transcription factor enrichment analysis was performed using ChEA3.