Update README.md

README.md

 # Vavassori_LNP2022_RNAseq_lnps
 
+Vavassori V, Ferrari S, Beretta S, et al.
+**Lipid nanoparticles improve ex vivo gene editing of human hematopoietic cells.**
+2022.
+
+Whole transcriptomic analysis 24 hours after treatment of CD4+ T cells from 3 healthy donors and of HSPC (form 3 replicates) for CD40LG editing treated with LNPs. As controls, cells untreated (UT), mock electroporated or treated with LNPs formulated without RNA (Empty LNPs) were employed.
+
+---
+
+### Analyses ###
+
+Stanrdard RNA-seq pipeline on 36 samples: 18 samples of T cells and 18 samples of HSPCs.<br>
+In details, for both cell types (i.e., T and HSPC) DGE analysis on samples was performed with DESeq2, comparing dfferent groups (adding donor covariate for T cells):
+```
+results(DESeq.ds, pAdjustMethod = "BH", independentFiltering = TRUE, contrast = c("groups", Group1, Group2), alpha = 0.05)
+```
+Enrichment on (positive or negative) differentially expressed genes (FDR < 0.05) and GSEA on pre-ranked gene lists (ordered by log2 Fold Change values) agasint the MSigDB Hallmark database were performed with ClusterProfiler:
+```
+enricher(PosDEGs, universe = GeneUniverse, pvalueCutoff = 0.05, TERM2GENE = HallMarkDB)
+
+GSEA(FullGenesOrderLogFC, TERM2GENE = HallMarkDB, nPerm = 10000, pvalueCutoff = 0.05)
+```
+
+---
+
+### Directories and Files ###
+
+- _paper_plots.R_: script used to produce the plots of the paper;
+- _paper_data_: folder with data used to produce the plots of the paper;
+- _GEO_RNAseq_lnp.xlsx_: GEO template file;
+- _config.yaml_: config files of the RNA-seq analysis pipeline.
+