RNA-seq for understanding astrocyte S1P1 signaling

Astrocytic S1P1 has been previously shown to be essential for FTY720 (an orally delivered drug for MS) efficacy (CNS), in addition to its well-known immunological mechanisms of action. FTY720-P (an analogue of S1P) is a functional antagonist to S1P1. TetTag c-Fos reporter mice displayed temporal and spatial GFP-labeling of astrocytic nuclei under experimental autoimmune encephalomyelitis (EAE) pathology. We generated astrocyte conditional S1P1-KO mice in c-Fos background (S1P1-AsCKOfos). In search of essential factors controlled by S1P-S1P1 signaling in astrocytes, we employed nuclear RNA-seq using RNA of DAPI+NeuN-GFP+ nuclei isolated from spinal cords (SCs) of EAE-induced WTfos, S1P1-AsCKOfos, and FTY720-treated WTfos mice. Overall design: A sequencing library was produced using 0.75 ng of the amplified cDNA from WTfos, S1P1-AsCKOfos and FTY720-treated WTfos EAE induced mice astrocytic nuclei. Each group had 4, 3 and 3 samples, respectively. Their transcript profiles were generated by deep sequencing using Illumina NextSeq500.