Project description:The objective of this study was to corroborate the findings of previous BRD-associated transcriptome experiments, utilizing multiple independent populations of high-risk beef cattle.
Project description:NanoString nCounter assay was performed to measure the basal expression of host response genes in primary human monocytes from convalescent COVID-19 donors and SARS-CoV-2 naïve healthy individuals.
Project description:Objective: Classify and further validate BRD-associated genes and mechanisms found to be differentially expressed at facility arrival in post-weaned beef cattle from multiple independent populations. Our approach was to profile and compare at-arrival whole blood transcriptomes of post-weaned beef cattle that failed to develop symptoms associated with clinical BRD and cattle that ultimately were diagnosed and treated for clinical BRD within the first 28 days of facility arrival, further stratifying diseased animals into severity cohorts. Methods: Whole blood RNA profiles were generated via NGS approach, using an Illumina Novaseq 6000. Individual samples were processed using an adaptation of the Revised Tuxedo Suite protocol (Tuxedo 2), then analyzed in R using edgeR with likelihood-ratio testing. Genes were considered differentially expressed with an FDR cutoff of 0.05. Downstream analysis involved PCA, gene ontology term enrichment, pathway analysis, protein-protein interaction networking, and IPA. Results: 132 differentially expressed genes were identified between all three cohorts. Biological processes and pathways primarily involved neutrophilic activity, antimicrobial killing, cell cornification, and inflammatory signaling/regulation. Conlusions: This study corroborated genes and pathways identified in our previous work, while providing novel genes and pathways for future analysis.
Project description:Transcriptional profiling of host immune response in brains of mouse model of cryptococcal post-infectious inflammatory response syndrome (cPIIRS), cPIIRS mice treated with Ruxolitinib, and naïve control mice using the NanoString nCounter Mouse Neuroinflammation Panel v1.0. NanoString nCounter assay was performed to measure the expression of neuroinflammatory genes in the brains of cPIIRS mice (C57BL/6Tac, 21 day post-infection) compared to cPIIRS mice treated with Ruxolitinib, and naïve mice.
Project description:Nanostring nCounter Human miRNA assay (v1) of esophageal mucosal biopsies from children with eosinophilic esophagitis and controls Individual esophageal mucosal biopsies from children with eosinoniphilic esophagitis and controls were analysed for detection of microRNA
Project description:Whole blood samples from 36 cattle, across two independent populations, were sequenced via a Illumina NovaSeq 6000 system. Samples were bioinformatically processed in a HISAT2/StringTie pipeline, and stratified based on treatment frequency for BRD (healthy, treated once, treated twice or more and/or died). Differential expression analysis was conducted in R, utilizing an additive, multifactor generalized linear model and blocking for paired samples and year. Genes were considered differentially expressed with an FDR cutoff of 0.10. The objective of this study was to identify differentially expressed genes and mechanisms within and across treatment cohorts overtime, and determine host expressional changes influenced by BRD within the first 28 days of facility arrival.