Table 3.

Significantly altered coding and non-coding RNAs at 0, 3, 6, 12, and 24 h of SPT16 depletion

Hours depleted	0	3	6	12	24
mRNAs up	3	58	214	1366	5398
mRNAs down	53	5	174	1932	5000
DHS-associated ncRNAs up	0	4	38	203	8743
DHS-associated ncRNAs down	0	0	34	323	5789
Putative eRNAs up	0	78	137	154	2701
Putative eRNAs down	0	0	21	122	2439
PROMPTs up	0	4	4	95	2984
PROMPTs down	0	0	0	59	1831

Control samples and SPT16-depleted samples were separately pooled between cell lines for downstream analyses. Only transcripts with an adjusted p-value of < 0.05 are displayed (analyzed with DESeq2). Data were analyzed for significance via a two-way ANOVA and corrected for multiple comparisons using Dunnett’s test. Significant differences between transcript class were not identified (p = 0.3579, 5.077% of total variation), while each class of transcripts was significantly altered over depletion time (p < 0.0001, 77.58% of total variation)