Project description:Transcriptional profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:DNA methylation profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:DNA methylation profiling of IAS subjects Lymphoblasts RNA isolated from Iowa Adoption Study participants to compare the relationship between DNA methylation and gene expression on a genome-wide scale
Project description:RNA-Seq provides an effective way to annotate and measure the transcriptome, but the combination of cost, analysis and end-mapping challenges has limited its adoption for high-throughput quantitation and annotation. Here, we present an integrated experimental and computational suite for transcriptome annotation and quantitation based on the sequencing of mRNA ends. It consists of: a novel, simple, one-step, strategy 5' RNA-Seq; an optimized library construction method for strand-specific 3' RNA-seq that reduces costs and time; and a complete computational analysis toolkit. We demonstrate the power and versatility of our approach to study the transcriptome of LPS stimulation in mouse dendritic cells, promoter structure of the TCRb locus in mouse T cells, and gene expression in circadian cycles in Drosophila. Our platform provides a comprehensive solution for high-throughput, cost-effective transcriptome quantification and end annotation. A study of 5' and 3' end RNA sequencing methods
Project description:The intrahepatic milieu is inhospitable to intraportal islet allografts, limiting their applicability to ameliorate Type 1 Diabetes (T1D). Islet viability in the subcutaneous space represents an unfulfilled paradigm that is crucial to ensure widespread adoption and safety of clinical islet transplantation. Herein we report that human islets transplanted subcutaneously uniformly promote long-term euglycemia when admixed with a device-free Islet Viability Matrix (IVM), through a previously unknown anti-apoptotic mechanism.
Project description:We identify c-Maf as an essential factor regulating adoption of RORgamma t+ and T follicular regulatory phenotypes in effector Tregs. Differential expression analysis demonstrates reduced signatures of both ROR gamma t+ Tregs and T follicular regulatory cells following regulatory T cell-specific c-Maf deletion.
Project description:Biomanufacturing remains financially uncompetitive with the lower cost but higher carbon emitting hydrocarbon based chemical industry. Novel chassis organisms may enable cost reductions with respect to traditional chassis such as E. coli and so open an economic rout to low emission biomanufacturing. Extremophile bacteria exemplify that potential. Salt tolerant halomonas species thrive in conditions inimical to other organisms. Their adoption would eliminate the cost of sterilising equipment. Novel chassis are inevitably poorly understood in comparison to established organisms. Rapid characterisation and community data sharing will facilitate organisms’ adoption for biomanufacturing. This paper describes baseline proteomics data set for Halomonas bluephagenesis TD01 under active development for biomanufactoring. The data record comprises a newly sequenced genome for the organism; evidence for expression of 1150 proteins (30% of the proteome) including baseline quantification of 1050 proteins (27% of the proteome) and a spectral library enabling re-use for targeted proteomics assays. Protein data is annotated with KEGG Orthology enabling rapid matching of quantitative data to pathways of interest to biomanufacturing.
