Table 1 Files provided for each entry in the collection.

Metadata

txt

Sample information containing the following columns: GSE, GSM, treatment, group, organism, biological_system, dose, dose_unit, time_point, time_point_unit, slide, array, dye, platform, filenames, (and donor).

Normalized expression matrix

txt

Ensembl IDs as row names, sample IDs (GSM) as column names. Values are log₂-transformed and normalized signal intensities resulting from the preprocessing for microarrays, and normalized read counts for RNA-Seq data, respectively.

Corrected expression matrix

txt

Ensembl IDs as row names, sample IDs (GSM) as column names. Values are log₂-transformed, normalized, and batch corrected signal intensities for microarrays. Only included for microarray-based entries for which applicable.

Unfiltered differential expression results

xlsx

Excel file containing a sheet for each comparison (experimental group vs. control group) in the data set entry. Each sheet is named “group-control” and contains the following columns: LogFC, AveExpr, t-statistic, P.value, adj.P.Val, B-statistic, score and ID, as specified in the output of the limma R package¹⁶ for microarrays. Columns available for RNA-Seq are ID, baseMean, logFC, lfcSE, stat, P.Value, adj.P.Val and adj.P.Val.no.ind.filt. Results contain all the genes in the platform after filtering and annotation.

Filtered differential expression results

xlsx

Excel file containing a sheet for each comparison with significantly differentially expressed genes with |logFC| > 0.58 and adj.P.Val < 0.05. Each sheet is named “group-control” and contains the following columns: LogFC, AveExpr, t-statistic, P.value, adj.P.Val, B-statistic, score and ID, as specified in the output of the limma R package¹⁶ for microarrays. Columns available for RNA-Seq are ID, baseMean, logFC, lfcSE, stat, P.Value and adj.P.Val. Only included for entries for which significantly altered genes were found.