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JsNetSeto

ABSTRACT: Netrostoma setouchianum (ebi kurage), genomic and transcriptomic data

PROVIDER: PRJEB72569 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12654644_1.fastq.gz	Fastqsanger.gz
	ERR12654644_2.fastq.gz	Fastqsanger.gz
	ERR12666658.fastq.gz	Fastqsanger.gz
	ERR13669967_1.fastq.gz	Fastqsanger.gz
	ERR13669967_2.fastq.gz	Fastqsanger.gz

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Erythroblastic islands foster granulopoiesis in parallel to terminal erythropoiesis

Project description:The erythroblastic island (EBI), composed of a central macrophage and surrounding maturing erythroblasts, is the erythroid precursor niche. Despite numerous studies, its precise composition is still unclear. Using multispectral imaging flow cytometry (IFC), in vitro island reconstitution, and single cell RNA-seq of EBI-component cells enriched by gradient sedimentation, we present evidence that CD11b+ cells present in the EBIs are neutrophil precursors specifically associated with bone marrow EBI macrophages, indicating that erythro-(myelo)-blastic islands are a site for terminal granulopoiesis as well as erythropoiesis and production of these lineages is dynamically regulated within this niche. We further demonstrate that the balance between these lineages is determined by pathophysiological conditions, favoring granulopoiesis during anemia of inflammation, or erythropoiesis after erythropoietin (Epo) stimulation. Finally, we provide the heterogeneous molecular profiling of EBI macrophages as revealed by Cellular Indexing of Transcriptome and Epitopes (CITE)-sequencing of mouse bone marrow EBIs at baseline and after Epo-stimulation in vivo. Altogether, these data demonstrate that EBIs serve a dual role as terminal erythropoiesis and granulopoiesis niches and the central macrophages adapt to the needs of stress erythropoiesis as well as granulopoiesis.

2022-07-22 | GSE196347 | GEO

Transcriptome analysis of erythroblastic island macrophages

Project description:The erythroblastic island (EBI), composed of a central macrophage and surrounding erythroid cells, was the first hematopoietic niche discovered. The identity of EBI macrophages has thus far remained elusive. Gene expression profiles of BM F4/80+Epor-eGFP+ macrophages suggest a specialized function in supporting erythropoiesis.

2019-05-31 | GSE127980 | GEO

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Project description:Gordius_albopunctatus, genomic and transcriptomic data

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Tropheryma whipplei proteome - Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme

Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.

2017-12-18 | PXD006238 | Pride

jsNetSeto

Project description:Netrostoma setouchianum (ebi kurage)

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Overexpression of human TLR8 alters the bone marrow erythropoietic niche and causes fatal anemia in SLE-prone mice

Project description:The goal of this study was to understand the cause of anemia in lupus prone mice expressing humn TLR8. This was found to be due to a block in erythroblast differentiation form the CFUE to proerythroblast stage, a step that occurs within erythroblastic islands. We analyzed 19,309 bone marrow EBI cells and 4,794 spleen EBI cells that formed 22 clusters of cells. We confirmed the block in CFUE differentiation and found a defect in central macrophages that caused failure of erythroblast adherence

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EMG-generated identifictations

Project description:Identification data generated by the EMBL-EBI Metagenomics (EMG) service

| PRJEB24173 | ENA

Transcriptomic analyses of anti-adipogenic effects of oleuropein in human mesenchymal stem-cells

Project description:The main goal of the present work was to use an in vitro adipogenic-differentiation mode, with mesenchymal stem-cells (MSC) from human bone-marrow, to study whole-transcriptomic differential gene-expression when such cells are induced to differentiate into adipocytes in absence or presence of oleuropein. See details below. This work is complementary to a previously published one (Casado-Daz et al, 2016): Casado-DÃaz, A., Anter, J., MÃ¼ller, S., Winter, P., Quesada-GÃ³mez, J. M. and Dorado, G. (2016): Transcriptomic analyses of adipocyte differentiation from human mesenchymal stromal-cells (MSC). Journal of Cellular Physiology 9999: 1-14. DOI: 10.1002/jcp.25472. It corresponds to EMBL-EBI ArrayExpress accession E-MTAB-4884.

2018-12-31 | E-MTAB-5211 | biostudies-arrayexpress

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