BXSB_mice_CD20_BZR_repertoire, Werner et al

We investigated if a short-term B cell depletion during the pre-clinical phase of SLE in BXSB mice influences the B cell receptor repertoire. We could show that male BXSB mice treated with an anti-CD20 monclonal antibody show reduced diversity for IgG VDJ recombinations.
To perform this analysis Next Generation Sequencing was performed by on the Illumina MiSeq platform using a pair of overlapping paired-end reads (2x300 bp). 20 % PhiX was added for improved performance. Paired-end reads were merged with the IgRepertoireConstructor (Safonova et al., 2015). Read Quality was ensured by FASTQC quality analysis by MultiQC (Ewels et al., 2016).
Molecular amplification fingerprinting (MAF) error correction was achieved with unique molecular identifiers (UMI) as part of the cDNA synthesis and Multiplex Primers. PCR sequencing errors were corrected by pattern matching and filtering sequences containing both UMIS and correcting sequencing errors without introducing bias to read counts.
Sequences were separated according to the individual immunoglobulin specific primers (TAK_402, TAK_403, TAK_IgM, TAK_IgA) and VDJ annotation was conducted with the IMGT/HighV-QUEST service (Alamyar et al., 2012). Sequences using the IgM, IgG1/2 or IgA specific primer were further analyzed with ARGalaxy immune receptor pipeline (IJspeert et al., 2017).

Folder contains final data analyzed by ARGalaxy