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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ATAC-seq)

ABSTRACT: Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ATAC-seq)

PROVIDER: PRJNA517962 | ENA |

REPOSITORIES: ENA

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC

Project description:Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC

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Project description:Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (RNA-seq)

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (ATAC-seq)

Project description:Genome Wides Association Studies (GWAS) have identified tens of thousands of associations between human genetic variation and common disease. Despite the abundance of GWAS associations, functional identification and characterization of causative variants and effector genes remains a challenging prospect. Human erythropoiesis provides a highly tractable model system for the development of tools for GWAS analysis. We have developed a three-phase protocol for differentiation of peripheral CD34+ Haematopoietic Stem Cells (HSC) into mature enucleating erythrocytes. This protocol has been characterized for it’s the changes observed morphologically, immunologically (by FACS) and epigenetically (by ATAC-seq, ChIP-seq, and RNA-seq). We have used this protocol to study the effects of common GWAS variants affecting red blood cell traits, and more severe mutations causing Type-1 Congenital Dyserythropoietic Anemia (CDA-I).

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (RNA-seq)

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC (NG Capture-C)

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Characterization of human erythropoiesis using ex vivo differentiation of CD34 HSC

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

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miRNA expression during UCB-CD34 cells erythropoiesis

Project description:We investigated the miRNA expression in ex vivo human erythroid cultures from umbilical cord blood (UCB)-derived CD34 cells. Hypothetically, the decline of certain miRNAs may promote erythropoiesis by unblocking expression of key functional proteins while the up-regulation of other miRNAs may block commitment to non-erythroid lineages. Therefore, discovering the patterns and sequence of miRNA expression during hematopoietic differentiation will provide insights about the functional roles of these tiny noncoding genes. Keywords: miRNA expression profiling

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ATAC-seq of immunophenotypic LT-HSC and ST-HSC from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

Project description:To investigate how ex vivo culture affects chromatin accessibility in cultured HSC, we performed the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-Seq) on cLT (CD34+CD90+CD45RA-) and cST populations purified from 8 day cultured lineage depleted cord blood (lin- CB) cells treated with 3-Factor (4HPR+UM171+SR1), U+S or 4HPR as well as untreated and vehicle-treated (DMSO) control populations. The subsequent ATAC-seq data was compared to chromatin accessibility signatures generated from uncultured hematopoietic stem and progenitor populations (Takayama, et al.). We found that ex vivo culture shifted cLT and cST cells isolated from control or untreated samples to a chromatin accessibility profiles not found in LT-HSC, suggesting some loss of a stem-cell associated chromatin state. By contrast, 4HPR-treated, to some extent, and 3-Factor-treated HSC maintained chromatin accessibility features of uncultured LT-HSC.

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