Clc genomics workbench software program

RNA libraries were generated using an Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific) according to the manufacturer’s instructions. The RNA libraries were then processed for an emulsion polymerase chain reaction (PCR) using an Ion OneTouch^TM system and an Ion OneTouch 200 Template kit v3 (ThermoFisher Scientific). Template-positive Ion Sphere^TM particles were enriched and purified for the sequencing reaction with an Ion OneTouch^TM ES system (ThermoFisher Scientific). The template-positive Ion Sphere^TM Particles were then applied to Ion PI^TM Chips (ThermoFisher Scientific), and high-throughput sequencing was performed using an Ion Proton™ Semiconductor sequencer (ThermoFisher Scientific). All of the sequencing data were mapped on a human reference genome sequence (GRCh37/hg19) using the Torrent Suite software program (ThermoFisher Scientific). An expression analysis of each sample was imported into the CLC Genomics Workbench software program (CLC bio, Aarhus, Denmark), and the significance of the differences among the samples was determined by an unpaired t-test.

RNA was purified using a mirVana miRNA isolation kit (Thermo Fisher Scientific). RNA libraries were generated using an Ion Total RNA-Seq kit v2 (Life Technologies) according to the manufacturer’s instructions. The RNA libraries were then processed for emulsion PCR using an Ion OneTouch^TM system and an Ion OneTouch 200 Template kit v3 (Life Technologies). Template-positive Ion Sphere^TM particles were enriched and purified for the sequencing reaction with an Ion OneTouch^TM ES system (Life Technologies). The template-positive Ion Sphere^TM particles were then applied on Ion PI™ chips (Life Technologies) and a high-throughput sequencing reaction was carried out using an Ion Proton™ semiconductor sequencer (Life Technologies). All of the sequencing data were mapped on a human reference genome sequence (GRCh37/hg19) using the Torrent Suite software program (Life Technologies). The expression analysis for each sample was imported into the CLC Genomics Workbench software program (CLC Bio, Aarhus, Denmark) and the significance of the differences among the samples was determined by an unpaired t-test. The gene ontology (GO) analysis was performed using the MetaCore software.

Basically, the analysis was performed using methods previously reported by our group^{23 (link)}. RNA libraries were generated using an Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific) according to the manufacturer’s instructions. Emulsion PCR was carried out with an Ion OneTouchTM system and an Ion OneTouch 200 Template Kit v3 (Thermo Fisher Scientific). Template-positive Ion Sphere™ particles were enriched and purified for the sequencing reaction with an Ion OneTouch™ ES system (Thermo Fisher Scientific). The template-positive Ion Sphere™ Particles were loaded onto Ion PI™ Chips (Thermo Fisher Scientific) and for high throughput sequencing with an Ion Proton™ Semiconductor sequencer (Thermo Fisher Scientific). Sequencing data were mapped on a human reference genome sequence (GRCh38/hg38) using the Torrent Suite software program (Life Technologies). The expression analysis was performed in the CLC Genomics Workbench software program (CLC bio, Aarhus, Denmark), and differences among the samples were determined using an unpaired Student’s t-test. The gene list describing fold change and p-value was uploaded to the MetaCore software (Clarivate Analytics, PA, USA, URL; https://portal.genego.com/, version 6.33.69110.), and then pathway analysis was performed.