Transcriptomic analyis of donor (B6:SJL.C20) and host follicular and marginal zone B cells after adoptive transfer of follicular B cells into into lymphopenic (Rag2-/-) or replete animals (C57BL6)

The generation of marginal zone (MZ) B cells is a Notch2 dependent process. We observed that transdifferentiation of follicular (FO) B cells to an MZ-like phenotype is dependent on a lymphopenic environment. We therefore adoptively transftered congenically marked SJL.C20 (CD45.1) mature naive FO B cells into either lymphopenic Rag2-/- or intact C57BL6 (CD45.2) recipient mice and recovered and double sorted intermediate phenotype (MZ-FO) donor B cells at day 4 post transfer from Rag2-/- recipients or both MZ and FO phenotype donor B cells at day 8 post transfer from both recipient groups and performed RNA sequencing. Overall design: Samples are double sorted donor (B6:SJL.C20) and host follicular and marginal zone B cells after adoptive transfer into lymphopenic (Rag2-/-) or replete animals (C57BL6). 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.