From 7016c201f8ce052e593d5a2754428ce49b3a4a7e Mon Sep 17 00:00:00 2001 From: Giorgia Giacomini Date: Mon, 8 Jan 2024 18:35:31 +0000 Subject: [PATCH] Update README.md --- README.md | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index d5eb32b..11f72b7 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,15 @@ # Amodio_Infertility_2024 Amodio G, Giacomini G, Boeri L, et al. **T cell exhaustion and senescence signatures characterize and differentiate infertile men** -### Analyses ### -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). +### Single-Cell RNA Sequencing Analysis ### +**scRNAseq** (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: +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 <1200 or >6000, were filtered out. - Normalization - - Default seurat settings [vignette] + - Default Seurat settings ([NormalizeData function])(https://satijalab.org/seurat/reference/normalizedata) - 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: @@ -22,10 +20,9 @@ Single-cell (from 10X Genomics) analysis of CD3+ T cells purified from the perip - Intra-cluster comparisons - ### Directories and Files ### - **Script**: R scripts used for the analyses - - `1_PreProcessing_Data.R`: Full object creation + - `1_PreProcessing_Data.R`: Preprocessing, cell filtering and Full object creation - `2_Infertility_scRNAseq_analysis.R`: - `3_SubsetAnalysis_Annotations.R`: subset analyses of T cells and cluster manual annotation - `4_ScoreAnalysis_TcellSubset.R`: -- GitLab