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CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [Smart-seq]

ABSTRACT: CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [Smart-seq]

PROVIDER: PRJNA722297 | ENA |

REPOSITORIES: ENA

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CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [Smart-seq]

Project description:Using Smart-seq2 single cell sequencing we reported that plasmablasts from dengue-infected individuals separate into 4 distinct clusters with distinct function.

2021-04-16 | GSE172176 | GEO

CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [10X Genomics]

Project description:Using 10X Genomics we identified B cells with a plasmablasts signature (based on CD38, CD27 and PRDM1 expression) and extract these cells to assign them to our Smart-seq analysis run in parallel.

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CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

Project description:CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

| PRJNA722298 | ENA

CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [10X Genomics]

Project description:CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function [10X Genomics]

| PRJNA722299 | ENA

CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

Project description:Clinically important broadly reactive B cells evolve during multiple infections. The phenotype and function of B cells re-activated after secondary infection is different compared to B cells activated after a primary infection. Here we studied CD27highCD38high plasmablasts from patients with a primary or secondary dengue virus infection. Three transcriptionally and functionally distinct plasmablast clusters were identified. The largest cluster 0/1 was plasma cell-related and contained cells coding for virus serotype cross-reactive antibodies of the IgG1 isotype, consistent with memory B cell activation during an extrafollicular response. In contrast, cells in clusters 2 and 3 expressed low levels of antibody genes and high levels of genes associated with oxidative phosphorylation, EIF2 pathway and mitochondrial dysfunction. Clusters 2 and 3, which we name T cell-dependent plasmablasts, showed a transcriptional footprint of T cell help, in line with activation from either naÃƒÂ¯ve B cells or memory B cells. Our results contribute to the understanding of the parallel B cell activation events that occur in humans after natural primary and secondary infection.

| EGAS00001005258 | EGA

CD27hiCD38hi plasmablasts are activated B cells of mixed origin with distinct function

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-04-16 | GSE172180 | GEO

CD27<sup>hi</sup>CD38<sup>hi</sup> plasmablasts are activated B cells of mixed origin with distinct function.

Project description:Clinically important broadly reactive B cells evolve during multiple infections, with B cells re-activated after secondary infection differing from B cells activated after a primary infection. Here we studied CD27highCD38high plasmablasts from patients with a primary or secondary dengue virus infection. Three transcriptionally and functionally distinct clusters were identified. The largest cluster 0/1 was plasma cell-related, with cells coding for serotype cross-reactive antibodies of the IgG1 isotype, consistent with memory B cell activation during an extrafollicular response. Cells in clusters 2 and 3 expressed low levels of antibody genes and high levels of genes associated with oxidative phosphorylation, EIF2 pathway, and mitochondrial dysfunction. Clusters 2 and 3 showed a transcriptional footprint of T cell help, in line with activation from naive B cells or memory B cells. Our results contribute to the understanding of the parallel B cell activation events that occur in humans after natural primary and secondary infection.

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CTCF binding in B cells and Plasmablasts

Project description:The mammalian CCCTC-binding factor (CTCF) regulates gene expression through the formation of higher order chromatin structures. Recent evidence has implicated a role for CTCF in regulating gene expression in the human MHCII locus. To investigate the role of CTCF in murine MHCII gene expression we mapped CTCF binding sites in B cells (MHCII+ cells) and Plasmablasts which are differentiated B cells that have silenced MHCII gene expression. These observations lead to the identification of differential CTCF binding during differentiation in these cell types and suggest mechanims of MHCII gene regulation. Comparison of CTCF binding in B cells and Plasmablasts in mice using ChIP-seq

2014-02-05 | E-GEOD-44637 | biostudies-arrayexpress

Single-cell RNA counting at allele- and isoform-resolution using Smart-seq3

Project description:Large-scale sequencing of RNAs from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states. However, current single-cell RNA-sequencing (scRNA-seq) methods have limited ability to count RNAs at allele- and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells. Here, we introduce Smart-seq3 that combines full-length transcriptome coverage with a 5’ unique molecular identifier (UMI) RNA counting strategy that enabled in silico reconstruction of thousands of RNA molecules per cell. Importantly, a large portion of counted and reconstructed RNA molecules could be directly assigned to specific isoforms and allelic origin, and we identified significant transcript isoform regulation in mouse strains and human cell types. Moreover, Smart-seq3 showed a dramatic increase in sensitivity and typically detected thousands more genes per cell than Smart-seq2. Altogether, we developed a short-read sequencing strategy for single-cell RNA counting at isoform and allele-resolution applicable to large-scale characterization of cell types and states across tissues and organisms.

2020-04-14 | E-MTAB-8735 | biostudies-arrayexpress

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Project description:To characterize histology-based transcriptional heterogeneity of human hepatoblastoma, Smart-3SEQ was used to perform RNA sequencing of distinct histologic regions isolated by laser capture microdissection from formalin-fixed paraffin-embedded primary human hepatoblastoma specimens.

2024-10-13 | GSE279385 | GEO

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