Analysis script of "Aging, inflammation and DNA damage in the somatic testicular niche with idiopathic germ cell aplasia".
The single testis samples were analysed following the standard Seurat workflow [https://satijalab.org/seurat/articles/pbmc3k_tutorial.html] and integrated with the integration workflow [https://satijalab.org/seurat/articles/integration_introduction.html].
We used Seurat program (v.3.1.5), within the R environment (v3.6.1).
In the Seurat folder you can find the main analysis script:
- Single samples iNOA/OA analysis:
seurat.analysis.singleSamples.ipynb - integration of iNOA samples:
azoospermia.integration.seurat.ipynb - integration of adults samples (3 iGCA + CTL from GSE):
iGCA_CTL_integration.R
In the GEOdatasets you can find a script for analysis of testis samples from the literature (several GSE accession codes) and identification of somatic cell: testis_dataset_all.R
In the Development folder you can find:
- the script for the integration of neonatal, prepubertal, adults and iGCA samples:
development.R - the script with the definition of the Stage signatures A, B, C and their expression levels in iGCA and CTL samples:
development_StagesLEY.R
In Tcell_characterisation folder you can find the script for Tcell characterisation according to GSE126030: Tcell.R
In the Receptor_Ligand_interactions folder you can find the script to prepare files for CellPhoneDB analysis ans plot the CellPhoneDB results: CellPhoneDB_prepare_plots.R
In the PaperPlot folder you can find the script for reproducing the paper figures: plotsNatComm.R
The scripts integration_function.R, mySeuratfunctions.R, utility_functions.R are a set of functions (mainly wrapper of Seurat functions) I use for the analysis workflow.