DOI: 10.6084/m9.figshare.26990908.v1
title: Additional file 6 of Molecular analyses of zebrafish V0v spinal interneurons and identification of transcriptional regulators downstream of Evx1 and Evx2 in these cells

description: Additional file 6: Supplementary Table 2. Hurdle Model Statistical Analyses of Differential Expression in Our Single-Cell RNA-Seq Atlas of V0v Spinal Interneurons From an Incross of Zebrafish evx1i232/+;evx2sa140/+ Heterozygous Parents. Statistically robust Hurdle modelling was performed to analyze differential gene expression between distinct cell populations in our 48 h post-mitotic V0v spinal interneuron single-cell RNA-seq atlas (see Fig 6A and Methods). Each Excel sheet corresponds to a distinct Hurdle model statistical comparison of differential gene expression. The specific comparison is indicated on the Excel page tab. WT1: WT Group 1; WT2: WT Group 2; M1: Mutant Group 1; M2: Mutant Group 2; M3: Mutant Group 3. On each page, column A lists the gene ID from the Lawson Lab zebrafish transcriptome annotation model V4.3.2 (50). Column B lists the gene symbol. (Note that skor2, neff1, isl1a, pou2f2a, pou2f2b and zfhx3b genes returned previous gene names in the Lawson annotation. For ease of comparison, the current gene names shown in this paper are given in column B, with the Lawson gene symbols shown in parentheses). Column C provides the P-value for the comparison. This has not been corrected for multiple testing. Column D provides the P-value corrected for multiple testing by the application of the False Discovery Rate (FDR) Benjamini Hochberg method (46). Column E shows the ratio of the least squares mean reads for the antecedent (first population, column G) versus the consequent (second population, column H) population in the comparison. Column F shows the fold-change. The fold-change is converted from the ratio values in column E. When the ratio in column E is greater than 1, the fold-change in column F is identical to the ratio in column E. When the ratio in column E is less than 1, the fold-change in column F is calculated using the formula: -1/ratio. Each row corresponds to a distinct gene symbol. Each sheet has been sorted by the fold-change value in column F, from smallest to largest value. Consequently, negative fold-change values are shown at the top of the sheet, followed by positive fold-change values in the middle, and N.C. fold-change values at the bottom of the sheet. Negative fold-change values occur when the least squares mean reads for the antecedent (first population in the comparison, column G) is less than the least squares mean reads for the consequent (second population in the comparison, column H), and so expression of that gene is upregulated in the consequent (second) population in the comparison. In contrast, positive fold-change values occur when the least squares mean reads for the antecedent (first population in the comparison, column G) is greater than the least squares mean reads for the consequent (second population in the comparison, column H), and so expression of that gene is upregulated in the antecedent (first) population in the comparison. N.C. The Hurdle model of differential expression analysis cannot be calculated. Usually this is because there is no or little expression in one population in the comparison.