Last updated: 2021-02-15

Checks: 2 0

Knit directory: Mouse_AAV_PGR_RNAseq_bulk/

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.


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.

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 a0187dc. 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:


Untracked files:
    Untracked:  Mus_musculus.GRCm38.96.fulllength.saf
    Untracked:  analysis/00.WorkFlowR_setting.R
    Untracked:  analysis/01.Generate_reference_genome.Rmd
    Untracked:  analysis/02.Trimming_and_Mapping.Rmd
    Untracked:  analysis/03.QC_and_CPM.Rmd
    Untracked:  analysis/04.MDS.Rmd
    Untracked:  analysis/05.EdgeR_and_ScatterPlot.Rmd
    Untracked:  analysis/06.GSEA.Rmd
    Untracked:  header.sam
    Untracked:  header.txt
    Untracked:  logCPM_mrna_fulllen_pe_strrev_q30.mx.AAV_PR.fix_filt.csv
    Untracked:  output/2020021_AAV_PR_RNA_samplesheet.txt
    Untracked:  output/mrna_fulllen_pe_strrev_q30.mx.AAV_PR.fix_filt
    Untracked:  output/mrna_fulllen_pe_strrev_q30.mx.AAV_PR.unfiltered
    Untracked:  output/mrna_fulllen_pe_strrev_q30.mx.chr
    Untracked:  output/pheno.matrix_allsample.txt

Unstaged changes:
    Deleted:    analysis/01.Generate_reference_genome

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 a0187dc evangelynsim 2021-02-15 wflow_publish(“analysis/index.Rmd”)
Rmd 9358928 evangelynsim 2021-02-15 Start workflowr project.

Mouse AAV-PGR Bulk RNA-seq

This site contains the results of the bulk nuclei RNA-seq analyses presented in “Sex-specific control of human heart maturation by the progesterone receptor”, which has been accepted for publication in Circulation (1 February 2021). Follow the links below to view the different aspects of the analysis.

Abstract

Background: Despite in-depth knowledge of the molecular mechanisms controlling embryonic heart development, little is known about the signals governing postnatal maturation of the human heart.

Methods and Results: Here, we analyze the transcriptome and chromatin accessibility landscape of the developing human heart from early gestation to adulthood and uncover striking sex differences in the transcriptional programs underlying cardiac maturation. Our data identify the progesterone receptor as a key mediator of sex-dependent transcriptional programs during cardiomyocyte maturation. Functional validation studies in human cardiac organoids and mice demonstrate the progesterone receptor drives sex-specific metabolic programs and maturation of cardiac contractile properties.

Conclusions: These data provide a blueprint for understanding human heart maturation in both sexes and reveal an important role for the progesterone receptor in human heart development.

Authors

Choon Boon Sim, Belinda Phipson, Mark Ziemann, Haloom Rafehi, Richard J. Mills, Kevin I. Watt, Kwaku D. Abu-Bonsrah, Ravi K.R. Kalathur, Holly K. Voges, Doan T. Dinh, Menno ter Huurne, Celine J. Vivien, Antony Kaspi, Harikrishnan Kaipanaickal, Alejandro Hidalgo, Leanne M.D. Delbridge, Rebecca L. Robker, Paul Gregorevic, Cristobal G. dos Remedios, Sean Lal, Adam T. Piers, Igor E. Konstantinov, David A. Elliott, Assam El-Osta, Alicia Oshlack, James E. Hudson, Enzo R. Porrello.

Analysis

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

Quality control