MOESM2 of Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis

Additional file 2: Table S1. TAIR IDs of custom selected references for each transcriptome permutation. Table S2. DESeq2 results summary of analysis without reference genes or with different reference sets (Custom selected, from T Czechowski, M Stitt, T Altmann, MK Udvardi and W-R Scheible [26], from B Zhuo, S Emerson, JH Chang and Y Di [11] or Commonly used references). Table presents the number of genes found up- and down-regulated in Table S3 to S5. Summary of the results of several analyses for all the genes evaluated in this article: Column A: TAIR ID; Column B: ranking calculated with geNorm with the function “selectHKs” from the R package “NormqPCR”; Column C: average TPM value; Column D: covariance of the TPM values; Column E: the difference of expression of a gene between two samples calculated with NormFinder; Column F: the common standard deviation of the expression of a gene between two samples calculated with NormFinder; Column G: stability measure from NormFinder; Column H: log2-transformed fold change of each gene calculated with DESeq2 without using reference genes; Column I: adjusted p value of the gene deregulation calculated with DESeq2 without using reference genes; Column J: sources that identified the gene as a reference, when more than one source selected the gene as reference they are separated by a “;”. Table S3. Permutation Mlp37347 vs Control; Table S4. Permutation Mlp124499 vs Control; Table S5. Permutation Mlp124499 vs Mlp37347. Table S6. Metadata of samples used; replicate identification, number of sequenced reads, average length of the separation between two paired reads, number of reads after trimming and filtering and number of aligned reads for each of the 4 replicates of the three samples used in this study.