Last updated: 2019-12-06

Checks: 2 0

Knit directory: bentsen-rausch-2019/

This reproducible R Markdown analysis was created with workflowr (version 1.4.0). 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: 7864c7b

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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/
    Ignored:    test_files/

Untracked files:
    Untracked:  analysis/figure_6.Rmd
    Untracked:  analysis/olig_ttest_padj.csv
    Untracked:  code/sc_functions.R
    Untracked:  data/bulk/
    Untracked:  data/fgf_filtered_nuclei.RDS
    Untracked:  data/figures/
    Untracked:  data/filtglia.RDS
    Untracked:  data/glia/
    Untracked:  data/lps1.txt
    Untracked:  data/mcao1.txt
    Untracked:  data/mcao_d3.txt
    Untracked:  data/mcaod7.txt
    Untracked:  data/mouse_data/
    Untracked:  data/neur_astro_induce.xlsx
    Untracked:  data/neuron/
    Untracked:  data/synaptic_activity_induced.xlsx
    Untracked:  olig_ttest_padj.csv
    Untracked:  output/agrp_pcgenes.csv
    Untracked:  output/all_wc_markers.csv
    Untracked:  output/allglia_wgcna_genemodules.csv
    Untracked:  output/bulk/
    Untracked:  output/fig.RData
    Untracked:  output/fig4_part2.RData
    Untracked:  output/glia/
    Untracked:  output/glial_markergenes.csv
    Untracked:  output/integrated_all_markergenes.csv
    Untracked:  output/integrated_neuronmarkers.csv
    Untracked:  output/neuron/
    Untracked:  suppglia.Rmd
    Untracked:  wc_de.pdf

Unstaged changes:
    Modified:   analysis/9_wc_processing.Rmd
    Modified:   analysis/figure_1.Rmd

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 R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd 7864c7b Full Name 2019-12-06 wflow_publish(“analysis/index.Rmd”)
html b92c3e1 Full Name 2019-12-06 Build site.
Rmd d86be31 Full Name 2019-12-06 wflow_publish(“analysis/index.Rmd”)
html 8877423 Full Name 2019-12-06 Build site.
html 0f82677 Full Name 2019-12-03 Build site.
html f4dd96b Full Name 2019-10-29 Build site.
html 9ba06e1 Full Name 2019-10-28 Build site.
Rmd 9e266e2 Full Name 2019-10-28 wflow_publish(“analysis/index.Rmd”)
html dba9dff Full Name 2019-10-28 Build site.
Rmd d0d418a Full Name 2019-10-28 wflow_publish(“analysis/index.Rmd”)
html 87b8ff4 Full Name 2019-10-28 Build site.
html 39bb8a8 Full Name 2019-10-28 Build site.
Rmd cca8a37 Full Name 2019-10-28 wflow_publish(“analysis/index.Rmd”)
html c5d7980 Full Name 2019-10-28 Build site.
Rmd 01d64b2 Full Name 2019-10-28 wflow_publish(“analysis/index.Rmd”)
html 39ace95 Full Name 2019-10-28 Build site.
Rmd 8ab4106 Full Name 2019-10-28 wflow_publish(“analysis/index.Rmd”)
Rmd 749ac66 dylanmr 2019-10-21 Start workflowr project.

Project overview

A single intracerebral ventricular injection of FGF1 induces permanent normalization of blood glucose levels in multiple rodent models of type 2 diabetes. To understand the effects of FGF1 and identify cell-type specific responses key to blood glucose normalization, we performed multiple high throughput transcriptomic analyses at different timepoints in cohorts of male ob/ob mice.


Experimental Design

All the results and plots presented in the pages below should be reproduceible on your computer.

Increased sampling 5 days post treatment confirms findings and reveals novel responses

  1. Astrocytes and oligodendrocytes are the most responsive cell types at day 5

  2. WGCNA on astrocytes confirms snRNAseq findings

  3. Tanycyte label transfer from Campbell et al.

  4. Tanycytes activate specific gene programs across the 3rd ventricle

  5. Oligodendrocyte label transfer from Castelo-Branco et. al.

  6. FGF1 increases a pool of differentiating oligodendrocytes

Bulk RNA-seq reveals chronic effects of FGF1

  1. FGF1 increases synaptic plasticity up to 42 days post treatment

Credits

This project was led by Dylan Rausch and Marie Bentsen at the University of Copenhagen NNF CBMR and University of Washington in the labs of Dr. Tune Pers and Dr. Michael Schwartz