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Table 1 Output list of NRSA

From: Nascent RNA sequencing analysis provides insights into enhancer-mediated gene regulation

   File name File description
Tables Known gene pindex.txt pausing information for each gene in all samples
normalized_pp_gb.txt normalized read counts in promoter-proximal and gene body regions for each gene in all samples
pp_change.txt differential expression results of genes within promoter-proximal region across two conditions
gb_change.txt differential expression results of genes within gene body region across two conditions
pindex_change.txt differential expression results of genes of pausing index across two conditions
Enhancer Enhancer.txt list of identified enhancers with annotation, predicted target genes from different strategies, and rank scores
Enhancer_center.txt list of enhancer centers
normalized_count_enhancer.txt normalized counts for each enhancer
Enhancer_change.txt differential expression results of enhancers across two conditions
Long_eRNA long_eRNA.txt identified long eRNAs (default: length > 10 Kb)
longeRNA-pindex.txt pausing information of long eRNAs for all samples
longeRNA-normalized_pp_gb.txt normalized read counts in promoter-proximal and gene body regions of long eRNAs
longeRNA-pp_change.txt differential expression results of promoter-proximal regions of long eRNAs across two conditions
longeRNA-gb_change.txt differential expression results of gene body regions of long eRNAs across two conditions
longeRNA-pindex_change.txt differential expression results of pausing index of long eRNAs across two conditions
Figures Known gene boxplot_ppdensity.pdf box plot of normalized read density of promoter-proximal regions for each sample
boxplot_gbdensity.pdf box plot of normalized read density of gene body regions for each sample
boxplot_pausingIndex.pdf box plot of pausing index for each sample
pindex_change.pdf heatmap of pausing index change across two conditions for genes with adjp< 0.05
heatmap.pdf heatmap of condition-dependent transcription changes around TSS for active genes
Reps_condition1.tif histogram for variation across samples within condition 1
Reps_condition2.tif histogram for variation across samples within condition 2
Enhancer signal_around_ehancer-center.pdf GRO/PROseq signal around enhancer center for all samples