title: Illumina HiSeq 1000 paired end sequencing
design: NMD-deficient: somatic deletion of  UPF1A
library_construction_protocol: Total RNA was extracted from cells grown on K. pneumoniae or the relevant feeding Escherichia coli strains with the TRIzol (Invitrogen) procedure, modified by the addition of glass beads. 100µg of total RNA went through purification of the poly(A) RNAs with the MicroPoly(A)purist kit (Ambion). 25% of the output was used in the following RT. mRNA reverse transcription was performed with the SuperScript III kit (Invitrogen) and the anchor-oligo(dT) primer 5’-GCCCACCAGAGCCGGCGGATTTTTTTTTTTTTTTTT-3’. After alkaline lysis of RNA and removal of the oligo(dT) primer with G-50 columns (GE Healthcare), single-strand cDNA molecules were extended with a poly(G) tail by a Terminal Transferase (NEB) following the producer's instructions. After phenol purification and ethanol precipitation, the single stranded DNA was turned into double strand using in the Phusion PCR enzyme (Finnzymes) and the anchor-oligo(dC) 5’-GCCCACCAGAGCCGGCGGACCCCCCCCCCCCCCCCC-3’. Double-stranded DNA was then purified using Qiagen PCR purification kit. cDNA libraries were then amplified by 15 cycles of PCR.