GSM3895916: Becn1-M-KO rep2; Mus musculus; RNA-Seq
Cervical lymph nodes or cervical lymphomas were removed, flash frozen on dry ice. Total RNA was used for mRNA isolation and cDNA library generation with miRNeasy micro Kit (Qiagen). On-column DNase digestion (DNase-Free DNase Set, Qiagen) was performed according to manufacturer protocols to prevent genomic DNA contamination. RNA and library preparation integrity were verified using a 2100 BioAnalyzer system (Agilent). Ribosomal RNA depletion was performed following the low input protocol by RiboMinus Eukaryote System v2 (ThermoFisher) with 500 ng total RNA input. Finally, libraries were prepared using the Ion Total RNA-Seq Kit v2 (ThermoFisher) with minor changes to the standard protocol. These included lower amplification cycles and the usage of entire fragmented RNA for cDNA synthesis.