+ +
++Last updated: 2023-04-20 +
++Checks: 2 + 0 +
+
+Knit directory: Hevesi_2023/
+
+This reproducible R Markdown +analysis was created with workflowr (version +1.7.0). 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 +c534a49. +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:
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+These are the previous versions of the repository in which changes were
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+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 + | ++c534a49 + | ++Evgenii O. Tretiakov + | ++2023-04-20 + | ++update README for the submission + | +
| +Rmd + | ++7782ffd + | ++Evgenii O. Tretiakov + | ++2023-01-21 + | ++Start workflowr project. + | +
This repository contains code and output of the analysis of +single-nuclei RNA sequencing data for the article Hevesi Z et al., +2023.
+Please see file CITATION in the root of your Git repo
+that contains the citation information.
To see the results of the analysis please visit the analysis website.
+We aimed to resolve if there is a matched expression of neuropeptide +receptor(s) and their ligand(s) between the sensory trunk of the +trigeminal nerve (Pr5) and the ventrobasal hypothalamus on postnatal day +7 (P7) in mice. We hypothesized that a coincidence of neuropeptide +expression and release from the ventrobasal thalamus and the cognate +receptor(s) for the specific neuropeptide(s) in trigeminal neurons could +allow for novel hypotheses be built on intercellular communication +between peripheral axons and their postsynaptic targets in the thalamus. +Thereby, this work can be informative of the developmental integration +of the whisker pathway, one of the major sensory modalities in +laboratory rodents. To this end, we used single-cell RNA-seq on cells +dissociated from the ventrobasal thalamus and Pr5 on P7.
+We tested this hypothesis by single-nucleus RNA-seq performed in +parallel on the ventrobasal thalamus and Pr5 at P7. At this +developmental stage, the ventrobasal thalamus contained two subtypes of +Slc17a6+(glutamatergic) neurons, one subtype of Gad1/Gad2+ (GABA) +neurons, astroglia, oligodendrocytes, and vascular components (n = 923 +nuclei isolated from n = 3 pups of mixed sex). Slc17a6+ neurons, which +we recognize as cortically projecting glutamate neurons, co-expressed +molecular components underpinning barrel map formation (e.g., Grin1, +Adcy1, Prkaca,99 Ache, Slc6a4) and a significant amount of the +thalamocortical neuronal marker Cck, while other neuropeptides/hormones +were absent or barely present (e.g., Npy, Sst). At the same time, we +harvested n = 731 nuclei from the Pr5 by micro-excision at P7, of which +∼98% expressed Slc17a6, thus qualifying, in total or in part, as +centrally-projecting sensory neurons. This neuronal cohort harbored axon +guidance molecules, and neuropeptide receptors.
+We suggest that neuropeptides, particularly galanin, could +participate in guidance decisions of Pr5 axons given the complementarity +of ligand-receptor expression patterns, and that Galr1 expression could +be a time locked feature for those neurons that actively undergo +neuritogenesis at a given time.
++ +
++Last updated: 2023-04-20 +
++Checks: 2 + 0 +
+
+Knit directory: Hevesi_2023/
+
+This reproducible R Markdown +analysis was created with workflowr (version +1.7.0). 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 +c534a49. +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: .DS_Store
+ Ignored: .Rhistory
+ Ignored: .Rproj.user/
+ Ignored: .cache/
+ Ignored: .config/
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+ Ignored: .snakemake/
+ Ignored: cellbender/
+ Ignored: cellbender_latest.sif
+ Ignored: cellranger/
+ Ignored: data/Pr5P7_clusters.h5ad
+ Ignored: data/THP7_clusters.h5ad
+ Ignored: fastq/
+ Ignored: mm10_optimized/
+ Ignored: souporcell/
+ Ignored: souporcell_latest.sif
+
++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 + | ++c534a49 + | ++Evgenii O. Tretiakov + | ++2023-04-20 + | ++update README for the submission + | +
| +Rmd + | ++7782ffd + | ++Evgenii O. Tretiakov + | ++2023-01-21 + | ++Start workflowr project. + | +
snakemake -f --use-singularity -prk --cores <FILL-IN-N-CORES> --resources nvidia_gpu=1 --singularity-args "--nv --bind <FILL-IN-PATH-TO-CLONED-REPO>" --rerun-incomplete --retries 1 --resources mem_mb=<FILL-IN-MEM>