Gene expression profiles of primary LN3 T-ALL cells and wild-type T-lineage cells from the thymus and spleen

T cell acute lymphoblastic leukemia (T-ALL) develops spontaneously in the thymus of LN3 mice and infiltrates secondary organs, including spleen. We found leukemia-associated myeloid cells from the spleens of overtly sick LN3 mice significantly support survival of splenic T-ALL cells, but not tumor-free splenic CD8+ T cells, in vitro. To determine gene signatures induced in T-ALL cells by tumor-supportive myeloid cells, but not induced in wild-type T cells, we transcriptionally profiled primary LN3 T-ALL cells from leukemic mice and T-lineage cells from tumor-free mice, isolated from thymuses and spleens, via RNA-sequencing. Thymic and splenic T-ALL cells were isolated from mechanically dissociated thymuses and spleens, respectively, of overtly sick LN3 mice. For controls, total thymocytes and splenocytes were purified from mechanically dissociated thymuses and spleens, respectively, from C57BL/6J tumor-free mice, and CD8+ T cells (purity 85-95%) were then isolated from the splenocytes using a negative enrichment kit for isolating mouse CD8 T cells. Total RNA was isolated using the RNeasy Mini Kit and RNA quality and concentration were assessed on an Agilent Bioanalyzer 2100 using the Eukaryote Total RNA Pico/Nano assay. mRNA was enriched from total RNA using the Poly(A)Purist Mag kit and RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina. 2 x 150 bp paired-end sequencing was run on Illumina HiSeq 4000, with an average of 29.7 million read-pairs per sample.