Transcriptomic analyis of isotype specific bone marrow and siLP IgA and IgAKO plasma cells as well as follicular and MZ B cells

Plasma cell gene expression is driven both by isotype and tissue location. In this series we examine gene expression of bone marrow IgA, IgM and IgG plasma cells as well as IgA plasma cells from small intestine lamina propria. To validate tissue specific gene expression we also include gene expression from lamina propria IgA-/- plasma cells. All plasma cell samples are from Blimp1+/GFP reporter animals and splenic follicular and marginal zone B cell gene expression have been added as reference populations. Overall design: Samples are double sorted IgM+, IgA+ and IgM/A- BM PCs, IgA+ siLP PCs and PCs from IgAKO siLP as well as splenic follicular and marginal zone B cells. cDNA was prepared from RNA with 3' polyA capture method. Transcript abundance was measured by Kallisto psuedo-alignment and normalized (voom) and differential expression was assessed using limma.