Multimodal Profiling of Lymphoma Cells

Global gene expression profiling (GEP) relied on Illumina Mouse WG-6 v2.0 (San Diego, CA, USA) Bead Chips and data analytical approaches described elsewhere.^{32 (link)} NFκB DNA-binding activity was determined with the help of EMSA.^{33 (link)} Western blotting followed a recently published protocol^{34 (link)} using antibodies listed in Supplementary Material and Methods. Capillary-based Sanger sequencing of Myd88^L252 and flanking regions relied on an ABI 3730xl (Thermo Fisher Scientific, Foster City, CA, USA) instrument provided by the HCCC Genomics Core. FISH was performed on metaphase chromosomes using gene-specific probes for Igh and Myc.^{23 (link)} Images were acquired using a DMRXA epifluorescence microscope equipped with a Sensys charge-coupled device camera (Roper Scientific, Trenton, NJ, USA). Surface expression of B cell and plasma cell markers was analyzed with the help of a FACSCanto II flow cytometer (Becton Dickinson (BD), San Jose, CA, USA)^{35 (link)} and antibodies in Supplementary Material and Methods. Non-specific Ab binding was blocked using rat serum (Jackson Immunoresearch, West Grove, PA, USA) and 10 μg 2.4G2 (BioXCell, West Lebanon, NH, USA). Data were analyzed using FlowJo (Tree Star, Ashland, OR, USA).