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 |