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Expression data of freshly isolated and sorted HSC populations from murine fetal liver or adult bone marrow [array]

ABSTRACT: Expression data of freshly isolated and sorted HSC populations from murine fetal liver or adult bone marrow [array]

PROVIDER: PRJNA723907 | ENA |

REPOSITORIES: ENA

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Expression data of freshly isolated and sorted HSC populations from murine fetal liver or adult bone marrow [array]

Project description:We isolated murine fetal liver and murine adult bone marrow and FACS sorted LT-HSCs, ST-HSCs and MPPs. We used global expression analysis by microarray to compare regulated genesets in different HSC populations in fetal and adult.

2023-04-30 | GSE173158 | GEO

RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.

Project description:Hematopoietic stem cells (HSC) has unique characteristic to self-renew and replenish the entire blood system. During development, HSCs originate in the aorta-gonads-mesonephros (AGM), from where they migrate into the fetal liver at E11. Once resided in fetal liver HSC proliferate extensively to make sufficient stem pool for adult life. Around birth, HSC from FL migrate to bone marrow (BM) which is major site of hematopoiesis for whole adult life. In contrast to FL HSC, BM HSC remain quiescence state and give rise to different blood cell type under normal homeostatic condition. It has shown that FL HSCs display significantly faster expansion kinetics when transplanted into lethally irradiate mice, compared with HSCs from adult BM. However, detail molecular mechanism behind the difference in self-renewal potential is not fully understood. Here, we present the genome-wide transcriptome analysis of more proliferative FL HSC compared to quiescent BM HSC using RNA-Seq platform.

2016-02-19 | E-MTAB-4034 | biostudies-arrayexpress

RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.

Project description:RNA-Seq analysis of LT-HSC isolated from fetal liver and adult bone marrow.

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Transcription profiling of rat freshly-isolated alveolar epithelial type I cells, freshly-isolated type II cells, and type II cells cultured for 7 days

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Transcriptome analysis of freshly sorted and expanded regulatory and conventional T cells

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ATF4 governs functional expansion of hematopoietic stem cells partially via Angptl3 in the fetal liver microenvironment (array)

Project description:In this study, we demonstrated that deletion of the activating transcription factor 4 (ATF4) resulted in severely impaired HSC expansion in the fetal liver at E12.5 and E15.5. In contrast, generation of the first HSC population in the aorta-gonad-mesonephros region at E11.5 was not significantly affected. Furthermore, the HSC-supporting ability of both endothelial and stromal cells in fetal liver was significantly compromised in the absence of ATF4. Gene profiling using RNA-seq revealed down-regulated expression of a panel of cytokines in ATF4-/- stromal cells, including angiopoietin-like protein 3 (Angptl3) and vascular endothelial growth factor-A (VEGFA).

2015-11-20 | GSE66381 | GEO

Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells.

Project description:Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amount of sample input that is required for deep and quantitative proteome profiling. This is especially true if the cells of interest need to be purified by fluorescence-activated cell sorting (FACS) and one wants to avoid ex vivo culturing. To address this need, we developed an easy to implement, streamlined workflow that enables quantitative proteome profiling from roughly 2 μg of protein input per experimental condition. Utilizing a combination of facile cell collection from cell sorting, solid-state isobaric labeling and multiplexing of peptides, and small-scale fractionation, we profiled the proteomes of 12 freshly isolated, primary murine immune cell types. Analyzing half of the 3e5 cells collected per cell type, we quantified over 7000 proteins across 12 key immune cell populations directly from their resident tissues. We show that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled. The low input proteomics methods we developed are readily adaptable and broadly applicable to any cell or sample types and should enable proteome profiling in systems previously unattainable.

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Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification

Project description:Late fetal hematopoietic failure results from ZBTB11 deficiency despite abundant HSC specification

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Transcriptome analysis of freshly sorted and expanded regulatory and conventional T cells

Project description:Transcriptome analysis of freshly sorted regulatory T cells (CD4+CD25+) and conventional T cells (CD4+CD25-) and of expansion cultures of regulatory T cells (CD4+CD25+CD45RA+) and conventional T cells (CD4+CD25-). Three biological replicates were performed of freshly sorted Treg and Tconv cells each. Four replicates of Treg expansion cultures sorted into CD45RA+/- subpopulations prior to RNA extraction were performed.

2009-05-20 | E-GEOD-14232 | biostudies-arrayexpress

Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure.

Project description:For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes.

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