software package and standardized rna seq analysis workflow array studio version 10.1.3.3  (OmicSoft Corporation)

Journal: Molecular cell

Article Title: Transcriptional responses to IFN-γ require Mediator kinase-dependent pause release and mechanistically distinct functions of CDK8 and CDK19

doi: 10.1016/j.molcel.2019.07.034

Figure Lengend Snippet: Key Resource Table

Article Snippet: Mix2 RNA-Seq data analysis software , Lexogen , .

Techniques: Virus, Recombinant, Transfection, Protease Inhibitor, Reverse Transcription, Isolation, Lysis, Gel Extraction, Plasmid Preparation, Western Blot, Expressing, Cloning, Software

Journal: Molecular Therapy Oncolytics

Article Title: Collateral Lethal Effects of Complementary Oncolytic Viruses

doi: 10.1016/j.omto.2020.06.017

Figure Lengend Snippet: Genes Encoding Key Regulators of Antiviral Pathways Are Upregulated in Established Tumors (A) Schema for whole-exome sequencing of CT26WT cells cultured with or without 100 U/mL IFNα 2 or from established tumors. RNA was isolated and sent for Illumina RNA sequencing. (B) Heatmap comparing 58 interferon-stimulated genes and inflammatory genes generated using the average FPKM of two independent samples, clustered according to average linkage and Euclidean distance. (C) Log 2 (fold change) of gene expression in the 58-gene panel comparing the IFN-treated cells and tumor cells with the untreated CT26WT in vitro .

Article Snippet: AIR: RNA-Seq data analysis software (Sequentia Biotech, Barcelona, Spain) was used to generate differential gene expression analysis based on the negative binomial distribution to generate fragments per kilobase of transcript per million mapped reads (FPKM) for each condition as previously described.

Techniques: Sequencing, Cell Culture, Isolation, RNA Sequencing Assay, Generated, Expressing, In Vitro