. 2017 Mar 20;6:e22767. doi: 10.7554/eLife.22767

Table 1.

Ikaros represses transcription by interfering with RNAP2 recruitment rather than elongation. Analysis of differential gene expression (adj. p<0.05) 360 min after 4-OHT-induced nuclear translocation of Ikaros in B3 cells, RNAP2 ChIP-seq, and the distribution of RNAP2 over the TSS and the gene body derived from RNAP2 ChIP-seq. RNAP2 occupancy was significantly decreased at only 40.3% (372 of 924) of genes downregulated at adj. p<0.05 but increased to 62% when considering only genes downregulated with adj. p<0.01 and a minimal log2 fold-change of 2. This suggests that the failure to detect decreased RNAP2 occupancy at the majority of downregulated genes may be due to the limited sensitivity of RNAP2 ChIP-seq compared to RNA-seq.

DOI: http://dx.doi.org/10.7554/eLife.22767.009

Table 1—source data 1. Numerical data used to generate Table 1.

DOI: http://dx.doi.org/10.7554/eLife.22767.010

elife-22767-table1-data1.xlsx^{(2.2MB, xlsx)}

DOI: 10.7554/eLife.22767.010

Gene expression	RNAP2 occupancy by ChIP
Gene expression	Global	TSS~gene body	TSS>gene body	TSS<gene body
Unchanged: 8799	Unchanged: 8125	8019	49	57
	Reduced: 405	378	11	16
	Increased: 269	256	10	3
Downregulated by Ikaros: 924	Unchanged: 549	520	12	17
	Reduced: 372	324	15	33
	Increased: 3	3	0	0
Upregulated by Ikaros: 855	Unchanged: 634	615	15	4
	Reduced: 6	6	0	0
	Increased: 215	200	13	2