DOI: 10.5281/zenodo.14519113
title: Atlas of nascent RNA transcripts reveals enhancer to gene linkages

description: Data associated with the paper "Atlas of nascent RNA transcripts reveals enhancer to gene linkages"

GitHub repository for the analyses: https://github.com/Dowell-Lab/DBNascent_Analysis

Below are the summaries of the files associated with this publication. 

 

1. muMerge calls for each paper used in the merging

paper_mumerge_calls

- The calls are separated by the bidirectional caller (dreg, tfit)

- In the folders are bed files (e.g. Allen2014global_hg38_dreg_MUMERGE.bed) for each paper and species (hg38, mm10)

 

2. Base content for regions called by dREG and Tfit in each paper in mouse and human

mumerge_base_composition

- The base content for each paper after the first round of muMerge

- The files contain the id and the base nucleotide content in 300bp around the center region (id, cg, at)

 

3. Bidirectional regions called by Tfit and dREG after merging. Regions are for mouse and human datasets. (See https://github.com/Dowell-Lab/bidirectionals_merged)

bidirectional_regions

- Bidirectional regions called after muMerge and filtering

- Calls for both human and mouse datasets are reported (hg38_tfit_dreg_bidirectionals.bed.gz and mm10_tfit_dreg_bidirectionals.bed.gz)

- The bed files are in bed6 format with the following columns:

chromosome, start, stop, bidirectional, number of papers a bidirectional was called, strand (it is . since bidirectionals are not stranded)

 

4. Metadata for samples used in the SPECS and correlation analysis

metadata

 - Sample metadata for filtered samples (human_samples_QC_GC_protocol_filtered.tsv.gz) in the downstream analyses 

 

5. SPECS scores across genes and bidirectional regions

specs_scores

 - The SPECS scores for all tissues analyzed (filt_qc123_all_specs_all.txt.gz) are reported,

 - Along with the maximum (filt_qc123_all_specs_maxval.txt.gz) 

 - And minimum SPECS scores (filt_qc123_all_specs_minval.txt.gz).

 - The SPECS scores were also split by disease vs non-disease samples

 - The TPMs summaries are also included

 

6. Normalized counts 

normalized_counts

 - Gene and bidirectional region normalized counts (gene_bidir_tpm.tsv.gz)

 

7. Bidirectional Region and gene pairs (See https://github.com/Dowell-Lab/bidir_gene_pairs)

bidirectional_gene_pairs

- Gene and bidirectional region pairs (dbnascent_pairs.txt.gz) across tissues in high-quality samples. 

- The pairs are reported in a bed12 file

   - Where the first 6 columns are gene coordinates and the following 6 are bidirectional coordinates.

   - The remaining columns are the summary statistics for correlation and the relationship between the gene and bidirectional.

  - Additional columns note whether the pair overlaps eQTLs from GTEx (eQTL) or polII ChIA-PET loops



transcript1_chrom : Gene chromosome

transcript1_start : Gene start coordinate

transcript1_stop : Gene stop coordinate

transcript_1 : Gene id

transcript1_score : Gene score (. since none was assigned)

transcript1_strand : Gene strand

transcript2_chrom : Bidirectional chromosome

transcript2_start : Bidirectional start coordinate

transcript2_stop : Bidirectional stol coordinate

transcript_2 : Bidirectional id

transcript2_score : Bidirectional score (i.e. the number of papers that support a bidirectional from muMerge)

transcript2_strand : Bidirectional strand (. since these are not stranded)

pcc : Pearsons correlation coefficient

pval : P-value

adj_p_BH : Adjusted p-value (Benjamini-Hochberg correction)

nObs : Number of observations in correlation analysis

t : T statistic

distance_tss : Distance between the gene start (TSS) and the bidirectional start coordinate

distance_tes : Distance between the gene stop (TES) and the bidirectional start coordinate

position : Is the bidirectional upstream or downstream of the TSS

tissue : Tissue id based on metadata for tissue-derived correlations (labeled All_samples if all samples are used)

percent_transcribed_both : Percent of the number of observed samples used in the analysis

pair_id : Gene:Transcript~Bidirectional pair name

gene_id : Gene id

chiapet : Binary indicator for whether pair overlaps overlap polII ChIA-PET 

gtex : Bindary Indicator whether a pair is overlapping GTEx pairs