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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