NUDT2 Disruption Elevates Diadenosine Tetraphosphate (Ap(4)A) and Down-Regulates Immune Response and Cancer Promotion Genes

Marriott, Andrew S.; Vasieva, Olga; Fang, Yongxiang; Copeland, Nikki A.; McLennan, Alexander G.; Jones, Nigel J.

Three independent samples of total RNA were prepared from both KBM-7 and NuKO cells. RNA extraction was performed using a Qiagen RNeasy mini kit with QIAshredder, and the quantity and quality determined using a Nanodrop and Agilent Bioanalyzer. For each of the six samples, 10 μg of RNA was DNase-treated using an Ambion TURBO DNA-free™ kit and subsequently purified using AMPure XP beads. 2 μg of the DNase-treated total RNA was then subjected to rRNA depletion using the Ribo-Zero Gold (Human/Mouse/Rat) kit and purified again with Ampure XP beads. Successful depletion was assessed using a Qubit fluorometer and Agilent 2100 Bioanalyzer and all of the depleted RNA was used for the RNA-Seq library preparation using the ScriptSeq v2 protocol. Following 15 cycles of amplification the libraries were purified using Ampure XP beads. Each library was quantified using Qubit and the size distribution assessed using the Agilent 2100 Bioanalyzer. The final libraries were pooled in equimolar amounts using the Qubit and Bioanalyzer data. The quantity and quality of each pool was assessed with the Bioanalyzer and by qPCR using the KAPA Library Quantification kit for Illumina platforms on a Roche LC480II Light Cycler according to manufacturer's instructions. The template DNA was denatured according to the protocol described in the Illumina cBot user guide and loaded at a concentration of 9 pM. Sequencing was carried out on one lane of an Illumina HiSeq 2000 with version 3 chemistry generating 2 × 100 bp paired end reads. Quality control was maintained with a 1% PhiX spike-in.