Fiumara_BasePrimeEd2022_WES

Fiumara M, Ferrari F, Omer-Javed A, Beretta S et al. Discovery and mitigation of genotoxic effects of base and prime editing in human hematopoietic stem cells. Nature Biotechnology 2023.

• Base Editors (HDR): GSE220753

Analyses

Sequencing data were analyzed with the BAR-Seq2 pipeline, with the following parameters:

• --trim-sequences --trim-opt '-m 50 -q 30' to trim low-quality bases and keeping sequences having length >50bp;
• --edit-distance 2;
• --min-count 2 to keep only barcodes having minimum count equal to 2.

The number of clones were calculated for each sample by normalizing the number of unique BARs by the sample VCN. SCID-repopulating cells (SRC) frequency (1 out of 'x') was calculated by dividing the HSPC t0 equivalent by the number of unique BARs retrieved in the long-term human graft in the BM.