low input RNA-sequencing of in vivo activated murine 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells

An analysis of 2D2-WT and 2D2-HDAC1-cKO mice indicates an important function of HDAC1 in regulating autoimmune diseases, in particular experimental autoimmune encephalomyelitis). The aim of this NGS experiment was to determine the transcirptome profile of in vivo activated 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells in the absence of HDAC1 following MOG/CFA footpad immunization. mRNA expression profiles of in vivo activated 2D2-WT and 2D2-HDAC1-cKO CD4+ T cells were generated by low-input RNA sequencing. Naïve 2D2-WT or 2D2-HDAC1cKO CD4+ T cells (CD45.2+) were transferred (i.v.) into CD45.1+ recipient mice. 18 hours after transfer mice were footpad immunized with a 1:1 emulsion of 1 mg/ml CFA/MOG35-55 peptide. Draining (popliteal) lymph nodes were isolated 4 days later and single cell suspensions prepared. Two mice were pooled for one biological replicate and three biological replicates were generated for each genotype. 500 2D2+ CD4+ T cells CD45.2+ cells were sorted and subjected to low-input RNA sequencing.