Last updated: 2021-02-19

Checks: 2 0

Knit directory: 2021_UoM_Yap_shRNA_nuclei_RNAseq_ATACseq/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 704a4cf

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 704a4cf. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


Ignored files:
    Ignored:    .Rproj.user/

Untracked files:
    Untracked:  Mus_musculus.GRCm38.96.fulllength.saf
    Untracked:  header.txt
    Untracked:  mouseATAC*bed.saf
    Untracked:  mouseATAC*bed.saf.pe.mx
    Untracked:  mouseATAC*bed.saf.pe.mx.chr
    Untracked:  mouseATAC*bed.saf.pe.mx.fix
    Untracked:  output/YAP_shRNA_D28_Proteomics_results.xls
    Untracked:  output/edgeR_atac_cov2_LacZvsYap.xls
    Untracked:  output/edgeR_rna_LacZvsYap.xls
    Untracked:  output/logCPM_mrna_fulllen_pe_strrev.mx.fix_filt.csv
    Untracked:  output/mouse2human.txt.sort
    Untracked:  output/mouseATAC_peaks_cov2.bed.saf.pe.mx.fix_filt
    Untracked:  output/mrna_fulllen_pe_strrev.mx.fix_filt
    Untracked:  output/pheno.matrix.txt
    Untracked:  output/pheno.matrix_cov2.txt
    Untracked:  output/sampleinfo.txt

Unstaged changes:
    Modified:   README.md

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd 704a4cf evangelynsim 2021-02-19 wflow_publish(c(“analysis/01.RNAseq_primary_analysis.Rmd”, “analysis/02.RNAseq_QC_and_CPM.Rmd”,
Rmd 16fb194 evangelynsim 2021-02-19 Start workflowr project.

Mouse AAV6:Yap-shRNA Bulk RNA-seq and ATAC-seq

This site contains the results of the bulk nuclei RNA-seq and ATAC-seq analyses presented in “Yap regulates skeletal muscle fatty acid oxidation and adiposity in metabolic disease”, which has been accepted for publication in Nature Communications (9 February 2021). Follow the links below to view the different aspects of the analysis.

Abstract

Obesity is a major risk factor underlying the development of metabolic disease and a growing public health concern globally. Strategies to promote skeletal muscle metabolism can be effective to limit the progression of metabolic disease. Here, we demonstrate that the levels of YAP are decreased in muscle biopsies from obese, insulin-resistant humans and mice. Targeted disruption of Yap in adult skeletal muscle results in incomplete oxidation of fatty acids and lipotoxicity. Integrated ‘omics analysis from isolated adult muscle nuclei reveals that Yap regulates a transcriptional profile associated with substrate utilisation. In line with these findings, increasing Yap abundance in the striated muscle of obese (db/db) mice enhanced energy expenditure and attenuated adiposity. Our results demonstrate a vital role for Yap in skeletal muscle as a mediator of skeletal muscle metabolism. Strategies to enhance Yap activity in skeletal muscle warrant consideration as part of comprehensive approaches to treat metabolic disease.

Authors

Watt K.I., Henstridge D.C., Ziemann M., Sim C.B., Montgomery M.K., Samocha-Bonet D., Parker B., Dodd, G.T., Bond S.T., Salmi, T.M., Lee-Young R.S., Thomson R.E., Hagg A., Davey J.R., Qian H., Koopman R., El-Osta A., Greenfield J.R., Watt M.J., Febbraio M.A., Drew B.G., Cox A.G., Porrello E.R., Harvey K.F. and Gregorevic P.

Analysis

The data analysis consists of a number of steps that are detailed in the scripts listed below.

3. Proteomics