Examination of PDGFRβ reactivity and KLF4 expression following cerebral ischemia

This repository was organised by Daniel Manrique-Castano, former postdoctoral fellow and current research data curation officer at the Digital Research Alliance of Canada.

Website: https://daniel-manrique.github.io/

GitHub: https://github.com/daniel-manrique

Contact: dmanriquecastano .at gmail.com

This repository hosts Quarto and Python notebooks (data handling and statistical models) associated with the research article "XXX". Raw/processed data and outputs are available in our Open Science Framework (OSF) repository (https:doi.org/10.17605/OSF.IO/74MQN).

Files

Naming conventions for notebooks (taking as example Confocal_20x_ROIs_Ki67-Pdgfrb_Coloc.qmd)

Confocal: Imaging type (available strings = Confocal, Widefield).

20x: Objective magnification (Available strings = 5x, 10x, 20x, 40x).

ROIs: Region of interest (Available strings = ROIs [regions of interest], Whole [whole brain], Ipsilateral [ischemic hemisphere]).

Ki67-Pdgfrb: Marker stained/analysed (available strings = multiple, depending on experiment).

Coloc: Analysis performed in notebook (available strings = multiple, depending on each experiment).

Confocal imaging analysis

Confocal_20x_ROIs_Ki67-Pdgfrb_Coloc.qmd: [Quarto notebook, R code] Analysis of Ki67/PDGFRβ colocalization in defined ROIs of PDGFRβ_TdTomato mice.

Confocal_20x_ROIs_Klf4-Pdgfrb_Coloc.qmd: [Quarto notebook, R code] Analysis of KLF4/PDGFRβ colocalization in defined ROIs of PDGFRβ_TdTomato mice.

Confocal_40x_ROIs_Pdgfrb_Morpho_Analysis.qmd: [Quarto notebook, R code] Morphological analysis of PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mice.

Confocal_40x_ROIs_Pdgfrb_Morpho_BatchScript.qmd: [Quarto notebook, Python code] Extraction of morphological features from PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mice.

Flow Cytometry analysis

FlowCytometry_Pdgfrb_Analysis.qmd: [Quarto notebook, R code] Analysis of FACS-sorted PDGFRβ-positive cells from the ischemic core of PDGFRβ_TdTomato mice.

FlowCytometry_Pdgfrb_Processing.qmd: [Quarto notebook, R code] Processing of .FCS (FACS-derived files) for the analysis of PDGFRβ-positive cells from the ischemic core of PDGFRβ_TdTomato mice.

Widefield imaging analysis

Widefield_10x_Ipsilateral_KO_CD31-ColIV_Inten.qmd: [Quarto notebook, R code] Analysis of CD31/ColIV intensity in the ischemic hemisphere of PDGFRβ_KLF4-KO brains and corresponding controls.

Widefield_10x_Ipsilateral_KO_Fish_Pdgfrb.qmd: [Quarto notebook, R code] Analysis of PDGFRβ by Fluorescence in situ hybridization (FISH) from PDGFRβ_KLF4-KO brains and corresponding controls.

Widefield_10x_Ipsilateral_KO_Klf4_Exp.qmd: [Quarto notebook, R code] Analysis of KLF4 expression in the ischemic hemisphere of PDGFRβ_KLF4-KO brains and corresponding controls.

Widefield_10x_Ipsilateral_Ki67-Pdgfrb_Coloc.qmd: [Quarto notebook, R code] Analysis of Ki67/PDGFRβ colocalization in the ischemic hemisphere of PDGFRβ_TdTomato mice.

Widefield_10x_Ipsilateral_Ki67_PPA.qmd: [Quarto notebook, R code] Point Pattern Analysis (PPA) of Ki67-positive cells in the ischemic hemisphere of PDGFRβ_TdTomato mice.

Widefield_10x_Ipsilateral_Klf4_Exp.qmd: [Quarto notebook, R code] Analysis of KLF4 expression in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_10x_ROIs_CD31-Pdgfrb_Coloc.qmd: [Quarto notebook, R code] Analysis of perivascular and parenchymal PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_10x_ROIs_Gfap-Pdgfrb_Covariance.qmd: [Quarto notebook, R code] Analysis of GFAP/PDGFRβ covariance in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_10x_ROIs_Gfap-Pdgfrb_Handling.qmd: [Quarto notebook, R code] Creation of point patterns from GFAP/PDGFRβ single cells detections in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_10x_ROIs_Flox-Cre_Fish_Pdgfrb.qmd: [Quarto notebook, R code] Analysis of PDGFRβ by Fluorescence in situ hybridization (FISH) in ROIs of KLF4-Flox and PDGFRβ-Cre mouse brains.

Widefield_10x_ROIs_KO_CD31-ColIV_Coloc.qmd: [Quarto notebook, R code] Analysis of CD31/ColIV-stained sections in defined ROIs of PDGFRβ_KLF4-KO mouse brains and corresponding controls.

Widefield_10x_ROIs_KO_Pdgfrb_TDA.ipynb: [Jupyter notebook, Python code] Topological Data Analysis (TDA) of PDGFRβ-positive cells in defined ROIs of PDGFRβ_KLF4-KO mouse brains and corresponding controls.

Widefield_20x_ROIs_KO_Picosirius.qmd: [Quarto notebook, R code] Analysis of Picosirius staining in defined ROIs of PDGFRβ_KLF4-KO mouse brains and corresponding controls.

Widefield_20x_ROIs_Pdgfrb_Haralick.qmd: [Quarto notebook, R code] Analysis of Haralick features of PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_20x_ROIs_Pdgfrb_Haralick_BatchScript.qmd: [Quarto notebook, Python code] Extraction of Haralick features from PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_20x_ROIs_Pdgfrb_TDA.ipynb: [Jupyter notebook, Python code] Topological Data Analysis (TDA) of PDGFRβ-positive cells in defined ROIs of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_EarlyKO_Pdgfrb-Gfap.qmd: [Quarto notebook, R code] Analysis of GFAP/PDGFRβ expression in the ischemic hemisphere of PDGFRβ_KLF4-KO mouse brains and corresponding controls.

Widefield_5x_Ipsilateral_Gfap-Pdgfrb_Covariance.qmd: [Quarto notebook, R code] Analysis of GFAP/PDGFRβ covariance (PPA) in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_Gfap-Pdgfrb_Covariance_str.qmd: [Quarto notebook, R code] Analysis of GFAP/PDGFRβ covariance (PPA) in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains with striatal-only lesions.

Widefield_5x_Ipsilateral_Gfap-Pdgfrb_Handling.qmd: [Quarto notebook, R code] Creation of point patterns from GFAP/PDGFRβ single cells detections in the ipsilateral hemipshere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_Gfap_Convex.qmd: [Quarto notebook, R code] Analysis of GFAP convex hull in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_Gfap_IntDen.qmd: [Quarto notebook, R code] Analysis of GFAP integrated density (IntDen) in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_KO_Structure.qmd: [Quarto notebook, R code] Analysis of hemispheric shrinkage/atrophy in the ischemic hemisphere of PDGFRβ_KLF4-KO mouse brains.

Widefield_5x_Ipsilateral_Pdgfrb_IntDen.qmd: [Quarto notebook, R code] Analysis of PDGFRβ integrated density (IntDen) in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_Pdgfrb_LowHigh.qmd: [Quarto notebook, R code] Analysis of PDGFRβ_Low and PDGFRβ_High-expressing cells in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Widefield_5x_Ipsilateral_Pdgfrb_LowHigh_Str.qmd: [Quarto notebook, R code] Analysis of PDGFRβ_Low and PDGFRβ_High-expressing cells in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains with striatal-only lesions.

Widefield_5x_Ipsilateral_Pdgfrb_Shrinkage.qmd: [Quarto notebook, R code] Analysis of hemispheric shrinkage/atrophy in the ischemic hemisphere of PDGFRβ_TdTomato mouse brains.

Additional files

PDGFR-B_Reactivity_SupplementaryTables.qmd: [Quarto notebook, R code] Contains supplementary tables showcasing the results of the fitted models.

references.bib [.bib file] Bibliography filed used ti generate citation/references in all Quarto notebooks.

science.csl [Citation Style Language file] This files contains the Science Journal citation style implemented in the notebooks. Please note this is style is not associated to the journal the original research article is publish in.

Supplementary material

Please refer to the OSF repository https:doi.org/10.17605/OSF.IO/74MQN to access the Raw/processed data to run the notebooks in this repository.