Extended Data Fig. 4: ATAC-seq and mRNA-seq analysis in spt-2 mutant worms.
From: The histone chaperone SPT2 regulates chromatin structure and function in Metazoa
a, Chromatin accessibility at CeSPT-2 non-target genes in spt-2KO-A and spt-2HBM adult worms, measured by ATAC-seq and expressed in reads per million. b, Expression levels of differentially accessible (DA) genes in spt-2KO worms, compared to non-DA genes (divided in quartiles). Boxes represent the interquartile range; the thick line represents the median; the whiskers extend up to 1.5-fold of the interquartile range. n = DA gene: 150; 1st quartile: 5536; 2nd: 5536; 3rd: 5536; 4th: 5536. Statistical testing: Mann–Whitney test with Benjamini-Hochberg correction. P values = DA vs 1st: < 10−16; DA vs 2nd: < 10−16; DA vs 3rd: < 10−16; DA vs 4th: < 10−7. c, Gene Ontology analysis of the DA genes in spt-2KO worms. ‘p.adjust’ values indicate Benjamini-Hochberg P values obtained through an hypergeometric test. d, Volcano plot of gene expression levels in spt-2 HBM versus wild type worms. Red points indicate genes with FDR<0.001 and log2 fold change >1 or <−1. e, qPCR analysis for the indicated genes, relative to cdc-42 expression. Each point indicates an independent replicate with worms harvested on different days, n = 4. The RNA used for the qPCR was harvested independently from the RNA used for the mRNA-seq analysis. Statistical testing: one-way ANOVA with Dunnett’s post-test. ns: P > 0.05, *: P < 0.05, ** P < 0.01, *** P < 0.0001. One-way ANOVA results, R06C1.4: P = 0.0038; Y57G11B.5: P = 0.0269; asp-1: P = 0.0035; ZK813.7: P = 0.0669; clec-66: P = 0.0255; C14C6.5: P = 0.0094; skr-10: P = 0.1607. Exact P values of Dunnett’s post-tests are reported in Supplementary Table 3. Data are represented as mean ± S.D. f, Expression levels of RNAi effectors genes.
