Strand-specific RNA-seq Library Preparation

Total RNA from ex vivo sorted or in vitro stimulated FO B cells was isolated with the RNeasy Plus Mini Kit (Qiagen), and mRNA was purified by two rounds of poly(A) selection with the Dynabeads mRNA purification kit (Invitrogen). The mRNA was fragmented by heating at 94 °C for 3 min in fragmentation buffer. The fragmented mRNA was used as template for first-strand cDNA synthesis with random hexamers and the Superscript Vilo First-Strand Synthesis System (Invitrogen). The second-strand cDNA synthesis was performed with 100 mM dATP, dCTP, dGTP and dUTP in the presence of RNase H, E. coli DNA polymerase I and DNA ligase (Invitrogen). The incorporation of dUTP allowed for specific elimination of the second DNA strand during library preparation, thereby preserving strand specificity^{60 (link)}.