Journal: PLoS Pathogens

Article Title: An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model

doi: 10.1371/journal.ppat.1007221

Figure Lengend Snippet: (A-B) RNA-seq analysis was performed using RNA isolated from 3 different tumors infected with either the WT or Δ3C viruses. The relative frequency of the IGH transcripts containing various different IGHV genes is shown for each tumor; the frequency of the dominant IGHV genes in IGH transcripts of normal cord blood is also indicated.

Article Snippet: RNA Seq data analysis was conducted by BioInfoRx (Madison, WI).

Techniques: RNA Sequencing, Isolation, Infection

Journal: PLoS Pathogens

Article Title: An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model

doi: 10.1371/journal.ppat.1007221

Figure Lengend Snippet: (A-B) The frequency of the TRBV gene reads in the RNA-seq analysis of different tumors was determined by comparing the number of reads from each individual TRBV gene to the total number of TRBV gene reads.

Article Snippet: RNA Seq data analysis was conducted by BioInfoRx (Madison, WI).

Techniques: RNA Sequencing

Journal: PLoS Pathogens

Article Title: An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model

doi: 10.1371/journal.ppat.1007221

Figure Lengend Snippet: RNA-seq reads were mapped to the EBV genomes of 2 different tumors infected with each virus type. The locations of the Cp promoter, and the EBER, EBNA2, BHRF1 and LMP1 transcripts are indicated above the EBV genome map.

Article Snippet: RNA Seq data analysis was conducted by BioInfoRx (Madison, WI).

Techniques: RNA Sequencing, Infection, Virus

Journal: PLoS Pathogens

Article Title: An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model

doi: 10.1371/journal.ppat.1007221

Figure Lengend Snippet: RNA was isolated from tumors infected with the WT- or Δ3C virus-induced lymphomas, and RNA-seq performed. Mouse cell transcripts were removed from further analysis, and the levels of human genes in each tumor type was compared as described in the methods. (A). The relative level of cellular gene transcripts in EBNA3C-infected tumors, versus WT virus-infected tumors is shown for PAX5 (a B cell-specific gene), and known EBNA3C target genes. The fold-change in cellular gene expression in EBNA3C-infected tumors versus WT infected tumors is indicated, as well as the p-value for each difference. (B). A gene set enrichment analysis (GSEA) plot for the “Hallmark_E2F_Targets” gene set is shown in Δ3C virus-induced lymphomas compared to WT virus-infected lymphomas. (C). The most downregulated genes in the “Hallmark_E2F_Targets” gene set are shown, along with the fold-change in Δ3C virus–infected versus WT virus-infected cells, and the associated p-value. (D). The relative expression levels of genes encoding proteins important for activation of cell cycle progression are compared in Δ3C virus–infected versus WT virus-infected tumors, and the p-value for differences indicated.

Article Snippet: RNA Seq data analysis was conducted by BioInfoRx (Madison, WI).

Techniques: Isolation, Infection, Virus, RNA Sequencing, Gene Expression, Expressing, Activation Assay

Journal: PLoS Pathogens

Article Title: An EBNA3C-deleted Epstein-Barr virus (EBV) mutant causes B-cell lymphomas with delayed onset in a cord blood-humanized mouse model

doi: 10.1371/journal.ppat.1007221

Figure Lengend Snippet: (A). Molecular signature pathway analysis of RNA-seq results obtained from Δ3C virus-induced lymphomas versus WT virus-induced lymphomas is shown. (B). Examples of genes included in the “GO_Immune_Response” gene set (boxed in ) that are of highly upregulated in the Δ3C virus–infected lymphomas relative to the WT virus-infected lymphomas are shown, and p-values are indicated. (C-G). qPCR was performed using cDNA isolated from Δ3C virus-induced lymphomas versus WT virus-infected lymphomas, using human specific primers to amplify genes shown in . Results were normalized to the level of GAPDH transcript. Standard error is shown. (H). IHC analysis using antibodies against EBNA2 (purple) and CCL5 (brown) in Δ3C virus-induced lymphomas was performed (Δ3C: SK1348). Examples of co-staining cells are indicated with arrows.

Article Snippet: RNA Seq data analysis was conducted by BioInfoRx (Madison, WI).

Techniques: RNA Sequencing, Virus, Infection, Isolation, Staining

Journal: iScience

Article Title: Fine-tuned KDM1A alternative splicing regulates human cardiomyogenesis through an enzymatic-independent mechanism

doi: 10.1016/j.isci.2022.104665

Figure Lengend Snippet:

Article Snippet: Artificial Intelligence RNA-Seq (AIR) Software , Sequentia Biotech , https://transcriptomics.cloud.

Techniques: Virus, Recombinant, Transfection, Protease Inhibitor, Magnetic Beads, cDNA Synthesis, Staining, Immunocytochemistry, Calcium Assay, Purification, Western Blot, Plasmid Preparation, Software, Electrophoresis, Microscopy, Imaging, Real-time Polymerase Chain Reaction, Mass Spectrometry

Journal: Database: The Journal of Biological Databases and Curation

Article Title: TISSUES 2.0: an integrative web resource on mammalian tissue expression

doi: 10.1093/database/bay003

Figure Lengend Snippet: In order to obtain confidence scores for each gene–tissue pair, we assess the relationship between raw expression values and fold enrichment, defined as the agreement between each dataset and gold standard datasets specific to the organism. The gold standard datasets are based on the UniProtKB protein tissue annotations in human, filtered for 1-to-1 orthologs between human and each of the three organisms. The x -axis contains raw expression values for gene–tissue pairs, in units specific to the type of experiment or processing of data (e.g. intensity units for microarray studies, FPKMs for RNA-seq), and averaged across bins of 100 pairs.

Article Snippet: The dataset produced at the Wageningen University under the FAANG project (Functional Annotation of Animal Genomes) consists of RNA sequencing data for eight porcine tissues and three different breeds (duroc, large white, pietrain).

Techniques: Expressing, Microarray, RNA Sequencing

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