Update README.md

README.md

-# Zonari_mPBHSCexp_2025_Barcoding
+# LV-Barcoding analyses
+
+This repository contains the key scripts used to generate the final tables and figures featured in the accompanying manuscript:  
+**Zonari et al**, _Expansion of Hematopoietic Stem and Progenitor Cells from Human Mobilized Peripheral Blood for Gene Therapy_, XXX, 2025.  
+
+## Abstract 
+Ex vivo expansion of mobilized peripheral blood (mPB) hematopoietic stem cells (HSCs)
+represents a promising approach to advance cell and gene therapy strategies yet is hampered by
+loss of stem cell function when applying commonly used culture protocols. We performed an indepth
+characterization of mPB expansion cultures by single cell RNA sequencing, which
+highlighted differentiation trajectories with preservation of lineage fidelity in committed
+progenitors. Defining a putative HSC cluster allowed an estimation of transduction efficiency in
+ex vivo cultures, which correlated with long-term gene marking in xenografts and patients enrolled
+in a gene therapy study. We then developed a clinically translatable, GMP-compliant process to
+expand lentivirus (LV)-transduced HSCs from mPB of pediatric patients and adult donors, by
+biologically informed protocol improvements of cytokine supplementation, media choice, timing
+of LV transduction and combinations of small molecules preventing the activation of
+differentiation programs. Our optimized process outperforms validated state-of-the-art cord blood
+expansion protocols when applied to mPB. LV integration site analysis and genomic barcodebased
+clonal tracking provided definitive proof for symmetric HSC self-renewal divisions
+occurring during ex vivo culture. These results warrant clinical testing of this HSC
+transduction/expansion process in an upcoming clinical gene therapy trial for autosomal recessive
+osteopetrosis (EU CT 2024-518972-30), addressing the need of obtaining a high number of
+functioning osteoclast progenitors for rapid bone marrow niche remodeling, where gene-corrected
+HSC can engraft and allow long-term disease correction.
+
+## Raw Data
+
+[DP-like_EX-U] :  [PRJEB76976](https://www.ebi.ac.uk/ena/browser/view/PRJEB76976). 
+[SCGM] :  [PRJEB77101](https://www.ebi.ac.uk/ena/browser/view/PRJEB77101).  
+[TD-Timing] :  [PRJEB77102](https://www.ebi.ac.uk/ena/browser/view/PRJEB77102). 
+
+## Repository structure
+
+In the main folder the main function for processing data produced by Barseq pipeline [Ferrari, Beretta et al, 2021](https://pubmed.ncbi.nlm.nih.gov/34031609/).  Below a glimpse of the file produced:  
+
+`
+Barcode      Count        SaturationPerc
+"TCTTTACTATAAAAAA"      19689   6.80
+"GGATGTCCCTTATAAT"      17875   12.97
+"TTAGGTTGTAATCATT"      14521   17.99
+"CGGAATAATTATTGGC"      14363   22.95
+"ATATTTACTATAACAC"      13786   27.71
+"TAGGATGAAACATTTG"      13764   32.46
+"TTACTAATTAATCTTA"      13425   37.10
+"TAAATTCATACAATCC"      5939    39.15
+"ACTGATGCTTCACGAA"      3067    40.21
+
+`
+
+This file (one for each sample) are then mainly processed by using the custom function [Charting_BCs_Light.R](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_barcoding/-/blob/main/ChartingBCs_Light.R) script and futherly analyzed with scripts present in each folder (one script for each experiment):  
+ 
+[DP-like_EX-U](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_barcoding/-/tree/main/DP-like_EX-U)  
+[SCGM](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_barcoding/-/tree/main/SCGM)   
+[TD-Timing](http://www.bioinfotiget.it/gitlab/custom/zonari_mpbhscexp_2025/zonari_mpbhscexp_2025_barcoding/-/tree/main/TD-Timing)  
+
+Processed data are stored in Data File 1,4,5 and 6.  
+
+