Gene expression profile at the single cell level of splenic LCMV-specific B cells in acute versus chronic LCMV infection [scRNA-seq, CITE-seq]

Chronic viral infection disrupts memory B cell development. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of antigen-specific B cells responding to acute versus chronic LCMV infection. Overall design: Splenic LCMV-specific B cells from LCMV-infected mice were isolated by fluorescence-activated cell sortings (FACS) and analysed using scRNA-seq. The only raw data which was used was the *.fastq.gz samples (6 pairs, 12 samples all together; out of them two pairs are for RNA-Seq - one for mice 24 and 44 and one for mice 36 and 59, 2 pairs for VDJ, again one for 27_44 and one for 36_59, and 2 pairs for HTO, again one for 27_44 and one for 36_59) and also the belo feature_reference.csv : id,name,read,pattern,sequence,feature_type C0301,C0301_TotalSeqC,R2,5PNNNNNNNNNN(BC),ACCCACCAGTAAGAC,Antibody Capture C0302,C0302_TotalSeqC,R2,5PNNNNNNNNNN(BC),GGTCGAGAGCATTCA,Antibody Capture Each of the 27_44 files contains a mixture of Acute replicate 1 and Chronic replicate 1, and the two can be distinguished by their HTO (C0301 representing acute and C0302 chronic). Similarly, each 36_59 file contains a mixture of Acute replicate 2 and Chronic replicate 2, and they again can be distinguished by HTO. The 10X software tool (Cellranger) created the not de-multiplexedCSP_27-44_filtered_feature_bc_matrix.h5 andCSP_36-59-filtered_feature_bc_matrix.h5 files. Since for each cell there we have its HTOwe know which one is acute and which one is chronic and based on this we can do the analysis The files linked to the Series records are the aggregation of the two sequencing runs (since after all the two replicates were analysed together).