Last updated: 2023-09-16
Checks: 2 0
Knit directory:
Mouse_endometrial_transcriptome_2023/1_analysis/
This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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 18c6463. 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: .gitignore
Untracked: 0_data/RDS_objects/DT.rds
Unstaged changes:
Modified: 0_data/RDS_objects/dge.rds
Modified: 0_data/RDS_objects/enrichGO.rds
Modified: 0_data/RDS_objects/enrichGO_sig.rds
Modified: 0_data/RDS_objects/fc.rds
Modified: 0_data/RDS_objects/lfc.rds
Modified: 0_data/RDS_objects/lmTreat.rds
Modified: 0_data/RDS_objects/lmTreat_all.rds
Modified: 0_data/RDS_objects/lmTreat_sig.rds
Modified: 0_data/RDS_objects/pub.rds
Deleted: 1_analysis/mmu04060.pv.png
Deleted: 1_analysis/mmu04151.pv.png
Deleted: 1_analysis/mmu04270.pv.png
Deleted: 1_analysis/mmu04510.pv.png
Deleted: 1_analysis/mmu04640.pv.png
Deleted: 1_analysis/mmu04670.pv.png
Modified: 2_plots/de/pval_1.05.svg
Modified: 2_plots/de/pval_1.1.svg
Modified: 2_plots/de/pval_1.5.svg
Modified: 2_plots/go/bp_dot_1.05.svg
Modified: 2_plots/go/bp_dot_1.5.svg
Modified: 2_plots/go/cc_dot_1.05.svg
Modified: 2_plots/go/cc_dot_1.5.svg
Modified: 2_plots/go/mf_dot_1.5.svg
Modified: 2_plots/go/upset_1.05.svg
Modified: 2_plots/go/upset_1.1.svg
Modified: 2_plots/go/upset_1.5.svg
Modified: 2_plots/ipa/Cell-To-Cell Signaling.svg
Modified: 2_plots/ipa/diseaseAndFunction.svg
Modified: 2_plots/ipa/pathways.svg
Modified: 2_plots/kegg/kegg_dot_1.05.svg
Modified: 2_plots/kegg/kegg_dot_1.1.svg
Modified: 2_plots/kegg/kegg_dot_1.5.svg
Modified: 2_plots/kegg/upset_kegg_1.05.svg
Modified: 2_plots/kegg/upset_kegg_1.1.svg
Modified: 2_plots/kegg/upset_kegg_1.5.svg
Modified: 2_plots/qc/PCA_IntvsCont.svg
Modified: 2_plots/qc/counts_after_filtering_3_3.svg
Modified: 2_plots/qc/counts_before_after_filtering_3_3.svg
Modified: 2_plots/qc/counts_before_filtering.svg
Modified: 2_plots/qc/library_size.svg
Modified: 2_plots/reactome/react_dot_1.05.svg
Modified: 2_plots/reactome/react_dot_1.1.svg
Modified: 2_plots/reactome/react_dot_1.5.svg
Modified: 2_plots/reactome/upset_react_1.05.svg
Modified: 2_plots/reactome/upset_react_1.1.svg
Modified: 2_plots/reactome/upset_react_1.5.svg
Modified: 3_output/enrichGO_sig.xlsx
Modified: 3_output/enrichKEGG_all.xlsx
Modified: 3_output/enrichKEGG_sig.xlsx
Modified: 3_output/lmTreat_all.xlsx
Modified: 3_output/lmTreat_fc1.5_voom2_all_fdr.xlsx
Modified: 3_output/lmTreat_sig.xlsx
Modified: 3_output/reactome_all.xlsx
Modified: 3_output/reactome_sig.xlsx
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 (1_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 |
---|---|---|---|---|
html | b44640a | Ha Manh Tran | 2023-01-23 | Build site. |
html | 8c9178d | tranmanhha135 | 2023-01-21 | added png |
html | d578f46 | Ha Manh Tran | 2023-01-21 | Build site. |
Rmd | 159f352 | tranmanhha135 | 2023-01-21 | adding for pathview |
html | 159f352 | tranmanhha135 | 2023-01-21 | adding for pathview |
Rmd | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
html | 4d51a4e | tranmanhha135 | 2023-01-20 | test png |
html | 691cf34 | Ha Manh Tran | 2023-01-20 | Build site. |
Rmd | b6cf190 | tranmanhha135 | 2023-01-19 | quick commit |
Rmd | 3119fad | tranmanhha135 | 2022-11-05 | build website |
html | 3119fad | tranmanhha135 | 2022-11-05 | build website |
Keywords: RNA sequencing, uterus, embryo implantation, endometrial receptivity, mouse
Author affiliations:
1 The Robinson Research Institute and Adelaide Medical School, University of Adelaide, Adelaide, SA 5000, Australia. 2 Hunter Medical Research Institute, Infertility and Reproduction Research Program, New Lambton Heights, NSW 2305, Australia. 3 Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, Discipline of Biological Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
* Corresponding author: Sarah A. Robertson, The Robinson Research Institute, Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia.
E-mail: sarah.robertson@adelaide.edu.au
Conflict of Interest Statement: The authors have declared that no conflict of interest exists
Receptivity of the uterus is essential for embryo implantation and progression of pregnancy. Acquisition of receptivity involves major molecular and cellular changes in the endometrial lining of the uterus from its non-receptive state at ovulation, to its receptive state four days later. The precise molecular mechanisms underlying this transition remain to be fully characterized. Here, we aimed to generate a comprehensive profile of the uterine transcriptome in the peri-ovulatory and peri-implantation states, and to define the differences between them, in the mouse. High throughput RNA-sequencing was utilized to identify genes and pathways expressed in the endometrium of unmated estrous female C57Bl/6 mice, and in female mice on day 3.5 post-coitum (pc) after mating with BALB/c males (n=3-4 biological replicates). Compared to the endometrium at estrus, 388 genes were differentially expressed in the endometrium on day 3.5 post-coitum (FDR ≤ 0.05). The transcriptional changes indicated substantial modulation of uterine immune and vascular systems during the pre-implantation phase, with the functional terms Angiogenesis, Chemotaxis, and Lymphangiogenesis predominating. Ingenuity Pathway Analysis software revealed several upstream regulators implicated in the transition to receptivity including various cytokines, steroid hormones, prostaglandin E2, and vascular endothelial growth factor A. This study confirms that the transcriptome of a receptive uterus is vastly different to the non-receptive uterus and identifies several genes, regulatory pathways, and upstream drivers in addition to those previously associated with implantation. This dataset will serve as a valuable tool and resource for future research on the molecular mechanisms of uterine receptivity.