KALLISTO estimated counts and LIMMA-fit values for time course expression profiles.

Excel-compatible tab-delimited text conforming to JavaTreeView extended CDT format. Each row is a transcript, with the UNIQID column giving the ucsf_hc.01_1.G217B systematic gene name. The NAME column gives short names taken from Data S1 of Voorhies, 2022 [70] with additional names and corrections based on human curation. The next 36 columns give KALLISTO estimated counts for each transcript in each sample. The next columns give LIMMA BH-adjusted p-values for differential expression in each of the 20 contrasts, and the corresponding LIMMA-fit log2 ratios are given in the final 20 columns. Description and HcG217B_pred (WUSTL G217B predicted gene accessions), HcG217B_rc (Edwards and colleagues. G217B transcript accessions [44]), and HcG217B_acc (UCSF1 gene accessions [70]); and Ryp1_ChIP, Ryp2_ChIP, Ryp3_ChIP, and Ryp4_C (indicating genes with promoters bound by Ryp TFs in Beyhan, 2013 [18]) are taken from Data S1 of Voorhies, 2022 [70]. UCSF2_acc and UCSF3_acc give gene accessions from the G217B assemblies of Heater, 2025 [24]. CR is “critical_region” for genes in the critical region, “chr7” for genes on chromosome 7 but outside of the critical region, and blank for all other genes. GWEIGHT is a placeholder column for JavaTreeView compatibility. The estimated counts in this file are sufficient to recapitulate the LIMMA analysis. (TXT)