DOI: 10.5281/zenodo.16545705
title: The Skeletal Muscle Epigenomic Landscape in Cardiorespiratory Fitness and Acute Exercise

description: This repository contains the processed data and summary results presented in my PhD dissertation, "The Skeletal Muscle Epigenomic Landscape in Cardiorespiratory Fitness and Acute Exercise." These files include results from RNA-Seq, ATAC-Seq, and CUT&Tag data generated from skeletal muscle tissue collected from HCR/LCR samples. All genomic coordinates are based on the rn7 reference genome. A description of all included files is provided below.

Background Information




Filename
Description


metadata_hcr-lcr_sample-phenotype-groups.txt
Phenotype and group information for the 128 HCR/LCR samples included in the study.


metadata_hcr-lcr_CUTTag-ATACSeq-libraries.txt
Batch information for HCR/LCR CUT&Tag and ATAC-Seq libraries, and conversion from unique library identifier to rat ID.


metadata_f2.txt
Data originally published in Ren et al. 2013, provided here to make phenotypic information about the F2 samples readily accessible for this study. 


ensembl-gene-info-used-in-the-hcr-lcr-study.txt
This file contains information about genes expressed in HCR/LCR skeletal muscle, including 1:1 Ensembl-to-gene symbol matching used in this project. Additional details include extended gene names and transcription factor status and family assignments based on the Animal Transcription Factor Database v4, as described in the thesis. This file is provided to facilitate replication of the Ensembl-gene symbol pairing used in the analyses.


motif-metadata.txt
Reference table for motifs used in this analysis, including internal IDs used between files within this repo (motif_id, dir_name), the source database identifying information to allow for motif lookup externally (data_source, altname), and motif information (ensembl, symbol).




Processed Data




Filename
Description


count-matrix_hcr-lcr_[modality].txt
Raw counts for features detected from sequencing-based modalities in the HCR/LCR study.


latent-variables.txt
Latent variables detected from background peaks and used to normalize counts.


inverse-normalized-counts_f2_[modality].txt
Inverse rank normalized counts for F2 samples used as the input for (e/ca)QTL analyses.


fst_hcr-lcr.txt
FST values calculated from the reference allele frequencies of each line, provided in the “HCR” and “LCR” columns.


genotypes_hcr-lcr.vcf.gz
Genotypes imputed from SNPs called from RNA-Seq data for the HCR/LCR samples.


genotypes_f2.vcf.gz 
Genotypes imputed from the Affymetrix Axiom panel for F2 samples.




HCR/LCR Results




Filename
Description


deseq-results_H3K27me3-H3K27ac-H3K4me1-H3K4me3-H3K36me3-ATACSeq-RNASeq.txt
Differential analysis results for all sequencing-based modalities.


Pk2Gene-links_significant-results.txt
Significant correlation links generated from the peak-to-peak-to-gene framework. These links are used to identify target genes of epigenomic peaks of interest.


pathway-enrichment_ChIP-Enrich-nearest-tss-results.txt
Pathway results from all epigenomic trials, when peaks were annotated to the gene with the nearest transcription start site.


pathway-enrichment_RNA-Enrich-results.txt
Differential gene expression pathway enrichment (RNA-Enrich) results.


pathway-enrichment_strong-enhancer-e4-clustered-heatmap.txt
Gene sets included in the heatmap that shows the reduced pathways in comparison to RNA-Seq and additional epigenomic modalities. This table includes representative cluster-to-child term pairs. These results were used to generate Figure 2.7c in the thesis.


pathway-enrichment_Pk2G-link-ranked-by-correlation-significance.txt
Pathway enrichment results probing Pk2G target genes of differential peaks, ranked by the significance of their correlation with the peak. The analysis was carried out four separate times for each direction of change (HCR up & LCR up), and Pk2G direction of relationship (positive & negative). These results were used to generate Figure 2.8c in the thesis. This file includes the representative cluster information included in the figure.


pathway-enrichment_global-differential-motif-enricher.txt
Over-representation analysis of Pk2G targets of peaks that contribute towards the differential motif enrichment when comparing HCR up peaks to LCR up peaks, stratified by motif, modality, direction of change between HCR/LCR, and direction of relationship with the target gene. These results were used to generate Figure 2.9c in the thesis, in which only gene sets included in that heatmap are provided in this table (FDR < 0.05 in at least one trial where > 1 gene resulted in the pathway).


pathway-enrichment_global-differential-motif_region-gene-input.txt
Region -> target gene pairs used for pathway enrichment input for the comparison of HCR up vs LCR up regions.


pathway-enrichment_broken-motif-enricher.txt
Over-representation analysis of Pk2G targets of peaks containing broken motifs. These results were used to generate Figure 2.11f in the thesis.


pathway-enrichment_broken-motif_region-gene-input.txt
Broken motifs residing within differential regions, with gene targets used for the allele-specific differential motif enrichment analysis. This file provides the variants that are fixed between HCR and LCR populations, which significantly change the potential binding affinity of TF motifs and are connected to differential abundance of chromatin accessibility or histone modifications.


f2_[e/ca]QTL-results.txt
Significant results from e/ca-QTL analysis (most significant variant-feature relationship returns FDR < 0.05), including variants with an LD r^2 > 0.5 to the most significant variant for each eGene or caVariant. Due to LD, there may be multiple variants that return the same strength and significance of relationship with the feature. The effect allele is designated as the HCR dominant allele, if that variant is present in the HCR/LCR analysis. The LD_r2 column provides the r^2 value of the remaining variants to the variant that is most significantly related to the feature. The af column is the allele frequency of the effect allele. The beta column is the strength and direction of relationship between the allele and gene expression or chromatin accessibility. The p_wald_rank column indicates the dense rank order of variant significance for each feature. The variant(s) with the most significant relationship with the feature have a p_wald_rank == 1. 


differential-motif-enrichment_[global/allele-specific].txt
Comparison of AME results for each of the individual trials of differential motif enrichment analysis. The trial_regions column indicates the modality and direction of change (if applicable) for each analysis.




Acute Exercise Results

Unless specified in the table, the resulting files provided alongside this chapter include results from all acute exercise contrasts of focus (e.g., MAX/REST, MAX/REC, REC/REST). 




Filename
Description


deseq-results_H3K27me3-H3K27ac-H3K4me1-H3K4me3-H3K36me3-ATACSeq-RNASeq.txt
Differential analysis results for all sequencing-based modalities, for exercise contrasts of MAX/REST, MAX/REC, REC/REST.


Pk2Gene-links_significant-results.txt
Significant correlation links identified within the acute exercise analysis.


Pk2G-links_fgsea.tsv
GSEA results when including gene targets of differential epigenomic regions, ranked by the absolute correlation coefficient.


pathway-enrichment_RNA-Enrich-results.txt
Differential gene expression pathway enrichment (RNA-Enrich) results.


pathway-enrichment_differential-motif_region-gene-input.txt
Motif->region->gene targets used as the input for over-representation analysis to interpret the differential motifs across each exercise state.


pathway-enrichment_differential-motif_enricher.txt
Over-representation analysis results by contrast, modality, motif, and direction of relationship between peaks and target genes.


MAXvRest-HCRvLCR-sig-gene-olap_overrepresentation-results.tsv
Intersection of HCR/LCR and exercise-responsive genes was used to carry out overrepresentation analysis, as described alongside Appendix Table 3 in the thesis.


differential-motif-enrichment_[contrast].txt
Comparison of AME results. Results from all modalities for each contrast are saved in individual files.


interaction_line-by-exercise_deseq-results_RNASeq.txt
Using the DESeq model, ~W_1 + train.sed + sex + grp + line + grp:line, differential results were obtained for HCR and LCR specific responses to exercise, as well as the interaction results. Line-specific results are indicated by either “HCR” or “LCR” in the sample_inclusion column. The “HCR_vs_LCR” value in sample_inclusion column denotes the interaction results.


interaction_line-by-exercise_RNA-Enrich-results.txt
RNA-Enrich results from the line:exercise interaction analysis, with trials labeled similarly to the DESeq results file.


interaction_train-by-exercise_deseq-results_RNASeq.txt
Using the DESeq model, ~W_1 + train.sed + sex + grp + line + grp:train.sed, differential results were obtained for training-specific responses to exercise, as well as the interaction results. Training-group specific responses to exercise are indicated by either “Train” or “Sed” in the sample_inclusion column, whereas the column value is set to “Train_vs_Sed” for the interaction results.


interaction_train-by-exercise_RNA-Enrich-results.txt
RNA-Enrich results for the train:grp interaction analysis, with trials labeled similarly to the DESeq results file.