Exon Level Expression Profiling: a Novel Unbiased Transcriptome
Ontology highlight
ABSTRACT: Transcriptome analysis of partially fragmented RNA from EndoC BH1 human beta cells sorted by FACs Global gene expression profiling has shown great promise in identifying altered cell differentiation status from cultured cells. However, FACs sorting cells using internal markers causes the RNA to be partially fragmented. Clariom D pico arrays are able to utilise partially fragmented RNA to provide exon level definition to determine changes in both total gene expression and splicing.
Project description:We report RNA Seq analysis using Illumina nextSeq500 of human beta cells EndoC-BH1 treated with FGF2 to induce dedifferentiation. FGF2 treatment induced dedifferentiation of EndoC-BH1 cells. Indeed, we observed a strong decrease in expression of β-cell markers, (INS, MAFB, SLC2A2, SLC30A8 and GCK). Opposingly, we identifed positive markers of human β cell dedifferentiation, as attested by increased expression of mature β-cell disallowed transcription factors (MYC, HES1, SOX9 and NEUROG3). Interestingly, our temporal analysis revealed that loss of expression of β cell specific markers preceded the induction of β cell disallowed genes.
Project description:EndoC-BH1 cells were plated in normal media and forward transfected with lipofectamine 3000 (2ug cDNA) of empty, OAS1, OAS2, or OAS3 plasmids from Vector builder
Project description:Responsiveness of EndoC-BH5 cells to cytokines was examined by RNA-seq of cells treated with IFNγ and IL1β for 24 h. The treatment resulted in profound changes in their transcriptome and upregulation of genes involved in the inflammatory pathwayand antigen processing and presentation, similar to previous studies on EndoC-BH1 cells and adult human islets. EndoC-BH5 cells hence represent a powerful tool to investigate the dialogue between beta cells and the immune system.
Project description:The aim of the study was to characterize the role of PCSK9 in human beta cells. We performed siRNA-mediated knockdown of PCSK9 in human beta cell line EndoC-bH1 and compared the expression profiles against control siRNA-treated cells.
Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 72 hours. The experiment was powered based PCSK9 knockdown in a pilot experiment. Sample size: 12x12.
Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 72 hours. The experiment was powered based PCSK9 knockdown in the pilot experiment [PXDxxx (PE083)]. Sample size: 12x12.
Project description:EndoC-bH1 cells proteomics was assessed in untreated baseline condition and after treatment with control siRNA at 24, 48 and 72 hours. Unpowered exploratory experiment. Sample size: triplicate per condition.
Project description:EndoC-bH1 cells were incubated with control siRNA or PCSK9 siRNA for 24, 48 and 72 hours. Untreated baseline samples were also included. Unpowered exploratory experiment. Sample size: triplicate per condition.