From 1111a506927a11a4868d4aff9546c1253837897c Mon Sep 17 00:00:00 2001 From: Stefano Beretta Date: Fri, 21 Oct 2022 13:55:00 +0000 Subject: [PATCH] Update README.md --- README.md | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/README.md b/README.md index b17ed26..8ec5d73 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,31 @@ # Vavassori_LNP2022_Proteomics +Vavassori V, Ferrari S, Beretta S, et al. +**Lipid nanoparticles improve ex vivo gene editing of human hematopoietic cells.** +2022. + +Mass-Spectrometry based proteomic analysis on T cells derived from 3 healthy donors, constituting 3 biological 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. + +- PRIDE: PXD037529 + +--- + +### Analyses ### + +Acquired raw data were analysed using MaxQuant, using the Andromeda search engine and a Human Fasta Database downloaded from UniprotKB. +For both group-specific and global parameters, all values were kept as default. +The LFQ intensity calculation was enabled, as well as the match between runs (MBRs) feature61. All proteins and peptides matching the reversed database were filtered out. +Resulting data were analyzed using the R/Bioconductor package DEP. +In details, protein quantification matrix from MaxQuant was processed and filtered keeping only proteins present in all replicates of at least one condition. +Then, after normalization using a variance stabilizing transformation (vsn), the imputation of missing values was done using random draws from a Gaussian distribution centered around a minimal value. +Differential Expressed Proteins (DEPs) among different tested conditions. + +Differential Expressed Proteins (DEPs) among different tested conditions were finally identified and the R/Bioconductor package ClusterProfiler was employed to perform pre-ranked Gene Set Enrichment Analysis (GSEA) on the Hallmark categories from the MSigDB. + +--- + +### 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. + -- GitLab