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MRNA profiles of hematopoietic stem and progenitor cells in bone marrow

ABSTRACT: Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Five thousand cells of subfractions within the HSC fraction were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

ORGANISM(S): Mus musculus

PROVIDER: GSE186956 | GEO | 2022/01/19

REPOSITORIES: GEO

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mRNA profiles of subfractions within hematopoietic stem cells in bone marrow

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: One hundred cells of subfractions within the HSC fraction were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

2022-01-19 | GSE187376 | GEO

ATAC-seq of subfractions within hematopoietic stem cells in bone marrow

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Fifteen thousand cells subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-seq using Hi-seq. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

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single ATAC-seq of subfractions within hematopoietic stem cells in bone marrow

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: One hundred thousand cells of subfractions within the HSC fraction were sorted. These cells were subjected to ATAC-sequence by using 10X Genomics Chromium Next GEM Single Cell ATAC Reagent Kits v1.1. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

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mRNA profiles of hematopoietic stem or progenitor cells in bone marrow after 5-FU administration

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 100 cells of HSCs were sorted. Moreover, after HSCs were cultured for 1day, 100 cells of phenotypic HSCs were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

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mRNA profiles of active hematopoieitc stem cells

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the activation of HSCs Methods: After wild type (WT) HSCs (CD150+ CD48- EPCR+ Lineage-) were treated with 5-fluorouracil (5-FU), 100 cells of HSCs were sorted. Moreover, after the culture with or without Nifedipien, cultured HSC fraction (CD150+ CD48- EPCR+ c-kit+ Sca-1+ Lineage-) were sorted. These cells were subjected to mRNA sequence using Next-seq (n>3). The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

2018-06-20 | GSE111118 | GEO

mRNA profiles of hematopoietic stem cells from p5 neonate and 4 weeks old mice.

Project description:Purpose: The goals of this study are to elucidate the underlying charactristic difference of p5 neonatal and 4 weeks old hematopoietic stem cell. Methods: p5 neonatal and 4 weeks old 100 cells of HSCs were sorted. Moreover, after HSCs were cultured for 1day, 100 cells of phenotypic HSCs were sorted. These cells were subjected to mRNA sequence using Next-seq. The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

2021-02-18 | GSE166911 | GEO

ATAC-seq of hematopoietic stem cells in bone marrow after 5-FU administration

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 15000 cells of HSCs were sorted. These cells were subjected to ATAC-seq using Next-seq. The sequence reads that passed quality filters were analyzed by FASTX-toolkit.

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CUT&Tag-seq for H3K27ac in hematopoietic stem cells in bone marrow after 5-FU administration

Project description:Purpose: The goals of this study are to elucidate the underlying mechanism for the regulation of HSC divisions. Methods: Before or after wild type (WT) mice were treated with 5-fluorouracil (5-FU), 12500 cells of HSCs were sorted. These cells were subjected to CUT&Tag-seq to analyze H3K27ac profile by using Next-seq. The sequence reads that passed quality filters were analyzed by Trimmomatic.

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mRNA profiles of hematopoieitc stme cells treated with interferon gamma and/or vitronectin

Project description:Purpose: The goals of this study are to elucidate the influence of integrin β3 signaling on STAT1-dependnet gene expression in IFNγ-treated HSCs. Methods: Wild type (WT) HSCs were cultured with or without IFNγ and/or VN in the presence of stem cell factor (SCF) plus thrombopoietin (TPO). Subsequently, cultured HSC fraction (CD48- c-kit+ Sca-1+ Lineage-) were sorted, followed by mRNA sequence using Ion Proton (n>4). Moreover, to extract genes whose expression were changed via STAT1 in the presence of IFNγ, mRNA profiles of STAT1-/- HSCs treated with or without IFNγ were also generated by the same way. The sequence reads that passed quality filters were analyzed by CLC genomic workbench. Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (build mm10) with CLC genomic workbench. Indeed, hierarchical clustering analysis showed that IFNγ-treated STAT1-/- HSCs was categorized to the group including Wt HSCs cultured in the absence of IFNγ rather than HSCs treated with IFNγ. Furthermore, gene set enrichment analysis (GSEA) showed that STAT1-dependent upregulated gene sets were significantly enriched within genes whose expression was enhanced in HSCs treated with VN and IFNγ. In contrast, integrin β3 signaling in the absence of IFNγ appears to not influence the expression of IFNγ/STAT1-dependent genes, as evidenced by the observation that VN treatment was statistically and significantly independent of the enrichment of gene sets that were both up-regulated by STAT1 Conclusions: Our study represents that STAT1 plays a central role in IFNγ-mediated HSC responses and integrin β3 signaling in HSCs promotes STAT1-dependent gene expression in the presence of IFNγ.

2017-06-01 | GSE81559 | GEO

Vanillin derivatives triggers oxidative stress and inhibit mitochondrial functions in Cryptococcus neoformans

Project description:Purpose: The purpose of this study is to define the mechanism of antifungal action of the vanillin derivative, o-vanillin, against Cryptococcus neoformans Methods: mRNA profiles of C. neoformasn cells cultured with or without o-vanillin were generated by RNA-Seq, using Illumina GAIIx. The sequence reads that passed quality filters were mapped to reference genome and the normalized RPKM values were calculated by CLC Genomics Workbench. Results: o-vanillin significantly altered global transcript profiles, induces oxidative stress, and interferes mitochondrial functions in C. neoformans. Conclusions: o-vanillin can be considered as the effective antifungal drug candidate. mRNA profiles of the cells grown in the presence or absence of o-vanillin were generated by RNA-Seq using Illumina GAIIx.

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