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RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

ABSTRACT: RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

PROVIDER: PRJNA515534 | ENA |

REPOSITORIES: ENA

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

| PRJNA515533 | ENA

ATAC-seq and RNA-seq of cord blood cells in cytokine-rich ex vivo culture conditions following sphingolipid modulation

Project description:ATAC-seq and RNA-seq of cord blood cells in cytokine-rich ex vivo culture conditions following sphingolipid modulation

| PRJNA515532 | ENA

RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

Project description:To elucidate the biological pathways altered by sphingolipid modulation with N-(4-hydroxyphenyl) retinamide (4HPR) treatment in human HSPC that may contribute to the restraint in proliferation while promoting persistence of HSC self-renewal as well as determine the mechanism of synergy in enhancement of HSC self-renewal with CB CD34+ agonists UM171 and StemRegenin 1 (SR1), we performed RNA-sequencing (RNA-Seq) of 3 pools of lin-CB cells following 2 or 4 days with DMSO, 4HPR, UM171+SR1 or 3-Factor (4HPR+UM171+SR1). We identified modulation of sphingolipid metabolism regulates self-renewal through activating coordinated stress pathways that coalesce on endoplasmic reticulum stress and autophagy programs.

2019-11-19 | GSE125213 | GEO

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.

2019-11-19 | GSE125212 | GEO

RNA-seq of cultured human hematopoietic stem and progenitor cells from umblical cord blood in cytokine-rich ex vivo culture conditions following sphingolipid modulation

| EGAS00001003756 | EGA

Proteomic and Phosphoproteomic Analyses of Yeast Reveal the Global Cellular Response to Sphingolipid Depletion

Project description:Sphingolipids are essential components of eukaryotic cells with important functions in membrane biology and cellular signaling. Their levels are tightly controlled and coordinated with the abundance of other membrane lipids. How sphingolipid homeostasis is achieved is not yet well understood. Studies performed primarily in yeast showed that the phosphorylation states of several enzymes and regulators of sphingolipid synthesis are important, although a global understanding for such regulation is lacking. Here, we used high-resolution mass-spectrometry-based proteomics and phosphoproteomics, in combination with data from a chemical genetic screen, to analyze the cellular response to sphingolipid synthesis inhibition. Our dataset reveals that changes in protein phosphorylation, rather than protein abundance, dominate the response to blocking sphingolipid synthesis. We identified Ypk1 signaling as a major pathway that is activated under these conditions, and we confirmed and identified Ypk1 targets. We also revealed key aspects of the cellular response to sphingolipid deprivation, including nodes that intersect with sterol metabolism and modification of lipid transport. Our data provide a rich resource for on-going mechanistic studies of key elements of the cellular response to the depletion of sphingolipid levels and the maintenance of sphingolipid homeostasis.

2016-12-23 | PXD003854 | Pride

ATAC-seq and RNA-seq of cord blood cells in cytokine-rich ex vivo culture conditions following sphingolipid modulation

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

2019-11-19 | GSE125214 | GEO

Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction | Plasma | Sprenger et al. 2025

Project description:Lipidomic analysis of plasma samples from aged rats +/- dietary intervention with an MFGM/EV-rich concentrate. In short, 10 plasma samples per intervention group were analyzed by MSaLL analysis. Uploaded data includes .raw files, ALEX123 search results, a sample list as well as a list with spike amounts of internal lipid standards. A detailed description of the analysis is provided in the publication with the title: Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction.

2025-04-10 | MSV000097591 | MassIVE

Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction | Kidney | Sprenger et al. 2025

Project description:Lipidomic analysis of kidney samples from aged rats with and without dietary intervention with an MFGM/EV-rich concentrate. In short, 9 or 10 kidney samples per intervention group were analyzed by MSaLL analysis. Uploaded data includes .raw files, ALEX123 search results, a sample list as well as a list with spike amounts of internal lipid standards. A detailed description of the analysis is provided in the publication with the title: Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction.

2025-04-10 | MSV000097597 | MassIVE

Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction | Lung | Sprenger et al. 2025

Project description:Lipidomic analysis of lung samples from aged rats with and without dietary intervention with an MFGM/EV-rich concentrate. In short, 8 or 10 lung samples per intervention group were analyzed by MSaLL analysis. Uploaded data includes .raw files, ALEX123 search results, a sample list as well as a list with spike amounts of internal lipid standards. A detailed description of the analysis is provided in the publication with the title: Dietary intake of a milk sphingolipid-rich MFGM/EV concentrate ameliorates age-related metabolic dysfunction.

2025-04-10 | MSV000097596 | MassIVE

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