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. 2018 Jan 15;32(2):96–111. doi: 10.1101/gad.309583.117

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© 2018 Li et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genes & Development, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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Figure 3. — Time-resolved analysis of transcript levels of genes containing EBF1-occupied sites within ±25 kb of transcription start sites before and after EBF1 induction (A,B). Up-regulated and down-regulated genes that change transcript levels >10-fold between 0 h and the pro-B stage are shown in A and B, respectively. Genes that are regulated by twofold to 10-fold are shown in Supplemental Figure S4, A and B. Individual transcript levels are shown in Supplemental Table S1 (>10-fold changes) and Supplemental Table S2 (twofold to 10-fold changes). Genes are organized into different clusters based on expression pattern using Short Time-series Expression Miner (STEM) (Ernst and Bar-Joseph 2006). Line plots (left panels) and box plots (right panels) are used to show fold changes (log₂ scale) and absolute expression levels (log₂ scale), respectively. Representative genes of each cluster are listed at the right. In each line plot, one representative gene is highlighted in red. (FC) Fold change; (FPKM) fragments per kilobase per million reads. (C,D) Dynamics of EBF1 occupancy around ±3 kb of EBF1 peaks that are associated with up-regulated genes (C) and down-regulated genes (D). Clusters correspond to the RNA-seq analysis. (E,F) ATAC signals around ±3 kb of EBF1 peaks associated with up-regulated genes (E) and down-regulated genes (F).