date: '2022-12-27'

Code used for the analysis of the RNA-seq datasets produced in this study. Original fastq files deposited in European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB59115.

Getting started

Different folders are included in this repository:

• RNA-seq_Park7_KnockOut_mice: Contains the analysis of 6 datasets including Park7 Knockout and wildtype mice: FemaleS 3 months of age, Males 3 months of age, FemaleS 8 months of age, MaleS 8 months of age first cohort, MaleS 8 months of age second cohort, MaleS 8 months of age first and second cohort together

• RNA-seq_Sex-differences_8months_mice: Contains the analysis of 1 dataset including male and female wildtype mice at 8 months of age

• RNA-seq_mouse_primary_astrocytes: Contains the analysis of 1 dataset of astrocytes treated with different siRNAs and their respective scramble: siPark7, siNfe2l2 and siCyp1b1 treated astrocytes

Specific questions:

• Gene dispersions by sex and cell type: RNA-seq_Sex-differences_8months_mice/Brain_sex_dispersion.qmd
• Cell purities and inflammation state: assess_cell_purity.qmd, using TPM on markers