@@ -5,6 +5,24 @@ Amodio G, Giacomini G, Boeri L, et al. **T cell exhaustion and senescence signat
Single-cell (from 10X Genomics) analysis of CD3+ T cells purified from the peripheral blood of men diagnosed with oligo-astheno-teratozoospermia (OAT, n=4), idiopathic non-obstructive azoospermia (iNOA, n=6), and a control group (FER, n=5).
**scRNAseq** analysis was performed using a standard [Seurat](https://satijalab.org/seurat/) pipeline that includes the following steps starting from a minimal object after loading of 10X data to markers identification:
- Preprocessing and cell filtering
- Each sample was pre-processed and cells with mitochondrial RNA percentages higher than 10 and a number of features <1200or>6000, were filtered out.
- Normalization
- Default seurat settings [vignette]
- Scaling:
- Data was regressed out by passing UMI count, the percentage of mitochondrial genes, the difference between the cell cycle phases scores.
- Dimensionality reduction and Harmony batch removal:
- A principal component analysis (PCA) with 100 principal components (PCs) was performed and a UMAP-representation as well as clusters were computed on the top 55 components (orig.ident as batch variable)
