Whole-transcriptome profiling of murine steady state CD69+ and CD69- memory CD8+ T cells from the bone marrow [expression microarray]

To understand the tissue-resident features of memory CD8+ T cell subpopulations isolated from the bone marrow according to the tissue retention marker CD69, we compared the global gene expression of ex vivo isolated CD69+ and CD69- bone marrow memory CD8+ T cells. Single cell suspensions were prepared from bone marrow of 8-week old untreated C57BL/L male mice. CD8+ T cells were enriched with anti-CD8a microbeads and the CD69+ and CD69- subpopulations of CD3+CD8+CD44+ memory cells were then FACS purified. Total RNA of isolated cells was extracted using a NucleoSpin RNA XS Kit (Macherey-Nagel) according to the manufacturer’s recommendations. Gene expression was analyzed using MG_U430_2 GeneChips (Affymetrix), according to the manufacturer’s recommendations. The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). The microarray analysis of gene expression was performed in house at the DRFZ as described before. Gene expression was quantified by RMA using the affy R algoroithm.