Ion proton s5 xl systems

Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described [10 (link), 31 (link), 32 (link)]. Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the UNM Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.

Total RNA was extracted from FFPE slices using the RNeasy FFPE kit (Qiagen) and the manufacture’s protocol. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech) and the Ion Plus Fragment Library Kit (ThermoFisher) as previously described (29 (link), 10 (link), 30 (link)). Sequencing was performed using the Ion Proton S5/XL systems (ThermoFisher) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center. RNA sequencing data is available for download from the NCBI BioProject database using study accession number PRJNA940178.

Total RNA was extracted from fresh frozen tissues (30 mg) using RNeasy Universal Kit (Qiagen, 19300 Germantown Road, Germantown, MD, USA) according to the manufacturer’s instructions. Synthesis of cDNA and library preparation were performed using the SMARTer Universal Low Input RNA Kit for Sequencing (Takara Bio, 1290 Terra Bella Ave., Mountain View, CA, USA) and the Ion Plus fragment library kit (Thermo Fisher, 168 Third Avenue, Waltham, MA, USA) as previously described [19 (link),20 (link),21 (link)]. Sequencing was performed using the Ion Proton S5/XL systems (Thermo Fisher) in the Analytical and Translational Genomics Shared Resource at the University of New Mexico Comprehensive Cancer Center. RNA sequencing data are available for download from the NCBI BioProject database using study accession number PRJNA433667. Sequencing was performed using the Ion Proton S5/XL system, which has been shown to give superior results with poor-quality RNA samples [19 (link),20 (link),21 (link)]. The RNA-seq reads were aligned to the human genome (hg19) using both the standard TMAP aligner as well as with STAR, a ‘splice-aware’ aligner [48 (link),49 (link)] that also detects candidate fusion reads mapped to more than one gene or chromosome.