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A glycan-based approach to cell characterization and isolation (bulk RNA-Seq)

ABSTRACT: A glycan-based approach to cell characterization and isolation (bulk RNA-Seq)

PROVIDER: PRJNA851754 | ENA |

REPOSITORIES: ENA

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A glycan-based approach to cell characterization and isolation

Project description:A glycan-based approach to cell characterization and isolation

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A glycan-based approach to cell characterization and isolation (scRNA-Seq)

Project description:A glycan-based approach to cell characterization and isolation (scRNA-Seq)

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A glycan-based approach to cell characterization and isolation (bulk RNA-Seq)

Project description:We leverage the extraordinary molecular diversity of modified heparan sulfate (HS) glycans to establish cellular glycotypes, defined by binding patterns of a panel of flow-cytometry compatible single-chain variable fragment antibodies (scFvs) specific for differentially modified HS. We find distinct glycotypes between closely related hematopoietic progenitors and lineages. The glycotypes of murine and human hematopoietic stem and progenitor cells (HSPCs) reveal dynamic yet similar HS modification patterns in vivo and in vitro, including along megakaryocyte and erythrocyte differentiation. Prospective HS scFv-based sorting identifies new cellular subtypes from both immunophenotypic megakaryocyte-erythrocyte progenitors and heterogeneous pools of HSPCs, thus offering additional discriminative power beyond conventional CD markers. Mechanistically, single-cell RNAseq revealed that a heptad of HS-related genes participate in megakaryocyte-erythrocyte fate determination and are reflective of the HS epitope recognized by specific HS scFvs. In summary, HS glycotyping establishes a role for HS modification patterns in hematopoietic lineage differentiation in mouse and human, and provides an orthogonal approach to define and isolate viable cell types across different cell lineages and species at unprecedented resolution.

2022-08-24 | GSE206670 | GEO

A glycan-based approach to cell characterization and isolation (scRNA-Seq)

Project description:We leverage the extraordinary molecular diversity of modified heparan sulfate (HS) glycans 8 to establish cellular glycotypes, defined by binding patterns of a panel of flow-cytometry compatible single-chain variable fragment antibodies (scFvs) specific for differentially modified HS. We find distinct glycotypes between closely related hematopoietic progenitors and lineages. The glycotypes of murine and human hematopoietic stem and progenitor cells (HSPCs) reveal dynamic yet similar HS modification patterns in vivo and in vitro, including along megakaryocyte and erythrocyte differentiation. Prospective HS scFv-based sorting identifies new cellular subtypes from both immunophenotypic megakaryocyte-erythrocyte progenitors and heterogeneous pools of HSPCs, thus offering additional discriminative power beyond conventional CD markers. Mechanistically, single-cell RNAseq revealed that a heptad of HS-related genes participate in megakaryocyte-erythrocyte fate determination and are reflective of the HS epitope recognized by specific HS scFvs. In summary, HS glycotyping establishes a role for HS modification patterns in hematopoietic lineage differentiation in mouse and human, and provides an orthogonal approach to define and isolate viable cell types across different cell lineages and species at unprecedented resolution.

2022-08-24 | GSE206671 | GEO

A glycan-based approach to cell characterization and isolation

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

2022-08-24 | GSE206672 | GEO

Development of a glycan microarray based method for ABO blood typing

Project description:Purpose: This study uses a high-throughput glycan microarray to develop a novel method to assign ABO blood type. The method will then be applied to samples from patients treated with PROSTVAC to determine if blood type correlates with survival Results: Many blood group A and B antigens correlate with blood type. Blood typing is best achieved using a combination of 10 signals Conclusion: ABO blood type can be determined with greater than 97% accuracy using only 4 microliters of serum.

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Resin and Magnetic Nanoparticle-Based Free Radical Probes for Glycan Capture, Isolation, and Structural Characterization.

Project description:By combining the merits of solid supports and free radical activated glycan sequencing (FRAGS) reagents, we develop a multifunctional solid-supported free radical probe (SS-FRAGS) that enables glycan enrichment and characterization. SS-FRAGS comprises a solid support, free radical precursor, disulfide bond, pyridyl, and hydrazine moieties. Thio-activated resin and magnetic nanoparticles (MNPs) are chosen as the solid support to selectively capture free glycans via the hydrazine moiety, allowing for their enrichment and isolation. The disulfide bond acts as a temporary covalent linkage between the solid support and the captured glycan, allowing the release of glycans via the cleavage of the disulfide bond by dithiothreitol. The basic pyridyl functional group provides a site for the formation of a fixed charge, enabling detection by mass spectrometry and avoiding glycan rearrangement during collisional activation. The free radical precursor generates a nascent free radical upon collisional activation and thus simultaneously induces systematic and predictable fragmentation for glycan structure elucidation. A radical-driven glycan deconstruction diagram (R-DECON) is developed to visually summarize the MS2 results and thus allow for the assembly of the glycan skeleton, making the differentiation of isobaric glycan isomers unambiguous. For application to a real-world sample, we demonstrate the efficacy of the SS-FRAGS by analyzing glycan structures enzymatically cleaved from RNase-B.

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Analysis of expression of genes involved in glycan and GBP synthesis in control and differentiated dendritic cells

Project description:Analysis of expression of genes involved in glycan and glycan-binding molecule synthesis in dendritic cells.

2011-04-29 | GSE28922 | GEO