GSM6758362: MMZt N+SAHA replicate 3; Zymoseptoria tritici; RNA-Seq
Cultures were centrifuged at 3000 rpm for 10 minutes and mycelium pellet washed with water was frozen with liquid nitrogen. Frozen mycelium was lyophilized and kept at -80°C until extraction. RNAs were extracted using Quiagen Plant RNAeasy Kit according to manufacturer protocol (Ref. 74904, Quiagen France SAS, Courtaboeuf, France).  PacBio Iso-Seq libraries preparation and sequencing was performed by the INRAE platform Gentyane (http://gentyane.clermont.inrae.fr). SMARTer PCR cDNA Synthesis Kit (ref 634926, Clontech, Mountain View, CA, USA) was used for polyA primed first cDNA strand synthesis followed by optimized PCR amplification and library preparation using SMRTbell Template Prep Kit (ref 101-357-000, Pacific Bioscience, Menlo Park, CA, USA) according to manufacturer protocols. The cDNA libraries were prepared without size selection and bar-coded for multiplexing. Sequencing was performed on a PacBio SEQUEL (version 1). Illumina RNA-seq single stranded libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490, New England BioLabs, Ipswich, Massachusetts, USA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765, New England BioLabs, Ipswich, Massachusetts, USA). Custom 8 bp barcode was added to each library during the preparation process. Sample were pooled and cleaned with magnetic beads included in the library preparation kit. The pool was run on a lane of Illumina HiSeqX (Illumina, San Diego, California, USA) using a 150-cycle paired end run