CD11c+ atypical B cells form an alternative memory B cell lineage, but the key transcription factors that drive their differentiation have not been identified. Here we established a novel CRISPR-Cas9 system to address this question. By co-nucleotransfecting target_gene_sgRNA and GFP_sgRNA ribonucleoprotein into Ighg2A10 knock in eGFP transgenic B cells (BCR specific to plasmodium surface circumsporozoite protein and express eGFP), we achieved 80-90% gene knock out efficiency of the target gene in eGFP knock out B cells. As a prove of concept, we knocked out Bcl6 by this method and transferred the cells into MD4 mouse followed by irradiated sporozoite immunization, and found 50-100 fold decrease of the germinal center B cell count in the spleen. Then we tested Zeb2, one of the highly expressed transcription factor in CD11c+ atypical B cells. Our result showed that Zeb2 knock out B cells only had mild reduction (~25%) in atypical B cell formation after immunization in vivo, suggesting the marginal role of Zeb2 in promoting the CD11c+ atypical B cell formation.