Fig. 1.

Schematic of experimental design and analysis. a Timeline representation of the drug treatment protocol, including the 1 h drug or DMSO (vehicle, V) pretreatment (initiated at − 1 h), administration of aqueous BDNF (B) or water (vehicle) treatment (Time = 0 h) and time of cell collection and RNA extraction (4 h). b 6-well plate showing each one of the 5 treatment groups and the abbreviations by which they will be referred to in the text: DMSO+Water (CTRL), DMSO+BDNF (V + B), 100 nM Ruxolitinib+BDNF (RX1 + B), 10 μM Ruxolitinib+BDNF (RX2 + B), 10 μM WP1066 + BDNF (WP + B). c Diagram represents the approach taken to identify differential gene expression (DEG) in response to JAK/STAT pathway inhibition. BDNF through its receptors activates multiple signaling pathways (represented by blue arrows) that impact transcription. Differential expression analysis comparing V + B vs. CTRL treatment groups (green box) will reveal the total set of genes that are regulated by BDNF-induced intracellular signaling pathways. To identify BDNF DEGs that are specific to JAK/STAT signaling, comparisons are made between the groups pretreated with JAK inhibitors (RX1 + B, RX2 + B, WP + B) and the group pretreated with vehicle (V + B) (purple box); DEGs from this comparison (where JAK/STAT inhibition reverses BDNF stimulation or inhibition) are thought to be associated with the JAK/STAT pathway