Transcriptome changes associated with elongation of bovine conceptuses II: differentially expressed transcripts in the endometrium on day 17 after insemination_JDS23399

The dataset provided contains supplemental files that are part of the article entitled: \"Transcriptome changes associated with elongation of bovine conceptuses II: differentially expressed transcripts in the endometrium on day 17 after insemination\". Supplemental Table S1. Complete list of transcripts evaluated using the Affymetrix Gene Chip Bovine Array.The smaller conceptus length category within each comparison was considered the reference group. The list of endometrium transcripts bore by different conceptus sex is also listed. Sex of each conceptus was determined based on the transcript abundance for XIST. Endometrium samples carrying female conceptuses are set as reference for the comparison (MvsF). ProbesetID = Affymetrix denomination for each probeset; gene symbol = recovered from the Ensemble database based on probesetID; EntrezGene = reference number for Bos Taurus recovered from NCBI database; Log2FC = Log2 fold-change; adj.P = P-value adjusted for false discovery rate; DET = dummy indicator identifying whether each transcript was differentially expressed (|Log2FC| ≥ 0.58; adj. P ≤ 0.05) for the referred comparison (0 = not differentially expressed; 1 = upregulated; -1 = downregulated). Supplemental Table S2. Complete list of diseases and biofunctions from the Ingenuity Pathway Analyses platform.The endometrium samples were classified based on the conceptus length which it was bearing. Each tab contains one of three comparisons: LvsS = large vs. small; MvsS = medium vs. small; LvsM = large vs. medium. The smaller conceptus length category within each comparison was considered the reference group. OP = P-value of overlap calculated using a right-tail Fisher’s exact test; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses. Predicted activation state was increased if ZS ≥ 2.00 or decreased if ZS ≤ -2.00. Supplemental Table S3. Complete list of canonical pathways from the Ingenuity Pathway Analyses platform. For comparisons involving size, the smaller conceptus length category within each comparison was considered the reference group. For the comparison involving sex, endometrium samples carrying female conceptuses were considered as the reference group. Ratio = proportion of the total number of molecules described for each pathway that were identified as DET in the study database; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses. Supplemental Table S4. Complete list of upstream regulators from the Ingenuity Pathway Analyses platform. . For comparisons involving size, the endometrium samples bearing smaller conceptus length within each comparison were considered the reference group. For the comparison involving sex, endometrium samples carrying female conceptuses were considered as the reference group. Expression log ratio = log fold-change for DET in the study database that were also predicted to be upstream regulators by Ingenuity Pathway Analyses; OP = P-value of overlap calculated using a right-tail Fisher’s exact test; ZS = Z-score for prediction of increased or decreased activation of biological functions based on the fold change of DET offered to the software; N/A = ZS not calculated by Ingenuity Pathway Analyses. Predicted activation state was activated if ZS ≥ 2.00 or inhibited if ZS ≤ -2.00.