Project description:Human in-vitro differentiated IgE+ and IgG+ Germinal Centre B cells, plasma blasts and plasma cells were isolated by flow cytometry and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform. B cells derived from 4 donors are submitted for each cell population.
Project description:Here we describe the dynamics underlying the generation of IgE-antibody secreting cells (ASC) in human nasal polyps (NP), mucosal tissues rich in ASC without germinal centers (GC). Using VH next generation sequencing, we identified an extrafollicular (EF) mucosal IgD+ naïve-like intermediate B cell population with high connectivity to the mucosal IgE ASC. Mucosal IgD+ B cells, express germline epsilon transcripts and predominantly co-express IgM. However, a small but significant fraction co-express IgG or IgA instead which also show connectivity to ASC IgE. Phenotypically, NP IgD+ B cells display an activated profile and molecular evidence of BCR engagement. Transcriptionally, mucosal IgD+ B cells reveal an intermediate profile between naïve B cells and ASC. Single cell IgE ASC analysis demonstrates lower mutational frequencies relative to IgG, IgA, and IgD ASC consistent with IgE ASC derivation from mucosal IgD+ B cell with low mutational load. In conclusion, we describe a novel mechanism of GC-independent, extrafollicular IgE ASC formation at the nasal mucosa whereby activated IgD+ naïve B cells locally undergo direct and indirect (through IgG and IgA), IgE class-switch.
Project description:This dataset contains 9 Illumina array spots representing 3 different treatment conditions of human mesenchymal cells. First two conditions in quadruplicate and third condition on single array. The data are intended to support blima package as testing data included in blimaTestingData package available at https://bitbucket.org/kulvait/blima page. The package was developed to make analysis of Illumina bead level data possible without summarizing them to the level of probes prior to differential expression testing.
Project description:Genome wide DNA methylation profiling of wild type and PPM1D mutant astrocytes and patient-derived DIPG cell lines. The Illumina Human EPIC Bead Array (850k) platform was used to obtain methylation beta values of over 850k CpG sites throughout the genome across a panel of DIPG cell lines.
