Data for: Stress and the brain transcriptome: identifying commonalities and clusters in standardized data from published experiments
Description
Supplementary Dataset 1. The dataset contains all retrieved data (full preprocessed dataset), information concerning experimental design and final result of re-annotation and gene name standardization. Supplementary Table 1. Summary of experiments included in the analysis. It also contains numerical codes used for identification of individual studies and transcriptomic comparisons concerning genotype, sex and stress-sensitivity of tested subjects, applied stress procedures, and analyzed brain areas. Supplementary Table 2. Ranking of stress-responsive genes. Supplementary Table 3. Referential list of GC-responsive genes. Supplementary Table 4. Calculation of gene expression enrichment in various cell types associated with the mouse nervous system based on data retrieved from http://mousebrain.org/genesearch.html. The analysis is restricted to genes belonging to choroid, meningeal and opalin cluster. Supplementary Table 5. Ranking of genes depending on duration of stress. Supplementary Table 6. Characteristics of stress-control comparisons containing genes from choroid and meningeal clusters. Included are only transcriptomic comparisons that contained at least 6 genes from either choroid or meningeal clusters. Supplementary Table 7. Ranking of genes with altered expression in animals that are vulnerable and resistant to stress. Supplementary Table 8. Sex-specific genes that are responsive to stress. Supplementary Table 9. Ranking of genes that are found both in animal models of stress and human PTSD patients. Supplementary Cluster Files 1. Cluster analysis of stress-responsive genes. Use Java Treeview software (https://sourceforge.net/projects/jtreeview/files/) to visualize data following guidelines provided in Supplementary Fig 2. List of experiments and their codes is available in Supplementary Table 1. Supplementary Cluster Files 2. Cluster analysis restricted to amygdala. Supplementary Cluster Files 3. Cluster analysis restricted to hippocampus. Supplementary Cluster Files 4. Cluster analysis restricted to nucleus accumbens. Supplementary Cluster Files 5. Cluster analysis restricted to prefrontal cortex. Supplementary Cluster Files 6. Cluster analysis restricted to mice. Supplementary Cluster Files 7. Cluster analysis restricted to rats. Supplementary Cluster Files 8. Cluster analysis restricted to acute stress. Supplementary Cluster Files 9. Cluster analysis restricted to prolonged stress (longer than 1 week). Supplementary Cluster Files 10. Cluster analysis restricted to stress of medium duration (from 2 to 7 days). Supplementary Cluster Files 11. Cluster analysis restricted to stress resilient animals Supplementary Cluster Files 12. Cluster analysis restricted to stress vulnerable animals.