Differential gene expression at shoot apices between Wild Type and vip3-1-null allele

The aim of this study was to evaluate gene expression defects at the shoot apical meristem and young flower meristems of the vip3-1 null allele. VIP3 belongs to polymerase II-associated factor 1 complex (Paf1c), which is involved in several RNA polymerase II-dependent transcriptional processes. Arabidopsis vip3 mutants exhibit phylotactic defects and strong floral indeterminacy phenotypes. Material for the RNA-seq was collected from the primary inflorescence of vip3-1 and Col-0 shoot apices (from plants grown in short day 21°C then continuous light 16°C conditions). Apices were dissected, by removing flower older than stage 4. Samples were collected into liquid nitrogen-cooled eppendorf tubes directly after dissection, each tube containing between 30 and 35 apices, 6 samples for each genotype. RNA extraction was performed using the PicoPure RNA Isolation kit Arcturus (ThermoFisher, KIT0204) with an on column DNAase treatment (Qiagen, catalog#79254). After elution, 2 samples were combined together, obtaining the final technical triplicates for each genotype. Isolated RNA was subjected to high throughput sequencing analyses to identify differentially expressed transcripts.