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RNA sequencing of undifferentiated iPS cells after culturing under graded zinc concentrations

ABSTRACT: RNA sequencing of undifferentiated iPS cells after culturing under graded zinc concentrations

PROVIDER: PRJNA638105 | ENA |

REPOSITORIES: ENA

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RNA sequencing of undifferentiated iPS cells after culturing under graded zinc concentrations

Project description:From our RNA-seq results, the metallothionein family members and several members of the mitochondrial ribosomal protein gene family are the top genes that are upregulated by increasing Zn concentration in human iPS cells.

2022-07-21 | GSE152017 | GEO

Transcriptome analysis reveals conditions for culturing human primitive undifferentiated spermatogonia

Project description:Transcriptome analysis reveals conditions for culturing human primitive undifferentiated spermatogonia

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Expression data from undifferentiated human iPS cell line, 201B7

Project description:In undifferentiated human ES cells, 5hr Met deprivation (delta Met) led to decreased proliferation, and promote differentiation We used microarrays to detail the mollecular mechanism of cell-death caused by Met deprivation in undifferentiated iPS cells.

2022-07-21 | GSE151795 | GEO

Transcriptome analysis reveals conditions for culturing human primitive undifferentiated spermatogonia

Project description:Spermatogonial stem cells (SSCs) are essential for the generation of sperm and have potential therapeutic value for male infertility, which afflicts >100 million men world-wide. To devise SSC therapy approaches, it is critical to first develop methods to culture human SSCs in vitro. Here, we report on a transcriptome approach to address this question. Using single-cell RNA-seq (scRNAseq), immunofluorescence, and germ-cell xenograft transplantation analyses, we identified a cell-surface protein, PLPPR3, that purifies human primitive undifferentiated spermatogonia (uSPG) enriched for SSCs. Comparative RNAseq analysis of PLPPR3+ cells (primitive uSPG) with KIT+ cells (enriched for differentiating [d] SPG) revealed that these two stages differentially express a remarkably large number of genes, including genes encoding key components in the TGF, GDNF, AKT, and JAK-STAT signaling pathways. Using scRNAseq analysis and conventional approaches, we tested the effect of manipulating these signaling pathways on cultured human SPG. This revealed that GDNF and BMP8B broadly support the culture of SPG, Activin A supports more advanced SPG, and one condition—AKT pathway inhibition—had the unique ability to selectively support primitive uSPG. These findings have implications for methods to culture and expand human SSCs for therapeutic uses in the future.

2020-06-29 | GSE144085 | GEO

Expression data from undifferentiated human iPS cell line, 201B7

Project description:Expression data from undifferentiated human iPS cell line, 201B7

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Impact of graded calorie restriction on mouse liver protein expression

Project description:Calorie restriction (CR) extends lifespan by modulating the mechanisms involved in aging. We quantified the hepatic proteome of male C57BL/6 mice exposed to graded levels of CR (0% to 40% CR) for three months, and evaluated which signaling pathways were most affected.

2023-10-24 | PXD033436 | Pride

Microarray of Aspergillus fumigatus wild type and ΔcrpA grown at different zinc concentrations.

Project description:Gene expression profiling of Aspergillus fumigatus comparing controls grown at normal zinc concentration of aspergillus minimum media (77uM), low (1uM) and high (500uM) zinc concentrations.

2019-08-15 | GSE135817 | GEO

Genome-wide nucleosome positioning maps from undifferentiated human iPS cells (hIPS) and iPS cells differentiated to neural progenitor cells (NPC).

Project description:We report the application of MNase-seq (Kent, Adams et al. 2011) to construct genome-wide nucleosome maps from human cells. To date, genome-wide changes in chromatin structure that occur during development in human cells have not been investigated widely. We have constructed and compared genome-wide chromatin maps from undifferentiated human iPS cells and and iPS cells differentiated to neural progenitor cells (NPC).

2019-04-24 | GSE117870 | GEO

Staphylococcus aureus lipoteichoic acid-stimulated undifferentiated and neutrophil-like differentiated HL-60 cells

Project description:HL-60 is a human promyelocytic leukemia cell line and differentiated HL-60 is an alternative to human primary neutrophils. The transcriptomic profile of undifferentiated HL-60 and dimethyl sulfoxide-differentiated HL-60 were determined at 4 and 24 hours after stimulation with high and low concentrations of Staphylococcus aureus lipoteichoic acids.

2023-12-15 | GSE239859 | GEO

Embryo response to different progesterone concentrations during superovulation of Holstein heifers

Project description:Greater progesterone (P4) concentrations during the follicular growth have been associated with greater quality of embryos produced by superovulated cows and heifers. However, it is yet to be determined the mechanisms by which oocyte exposure to greater P4 concentrations improves early embryo quality. The objective of this study was to evaluate the impact of different P4 concentrations during superovulation on the transcriptome profile of early bovine embryos. A total of 63 post-puberty Holstein heifers were randomly assigned into two experimental groups: High P4 (n = 31) and Low P4 (n = 32). Heifers received a pre-synchronization protocol followed by a protocol of superovulation that included the allocated P4 treatment. Embryo collection was performed 7 days post artificial insemination and embryos were evaluated for stage of embryonic development and grades of quality. Embryos graded as good/excellent quality (High P4: n = 27; Low P4: n = 27) were randomly allocated in 3 biological replicates per treatment group, balanced for stage of embryonic development. Transcriptome analysis suggested that exposure to different concentrations of P4 during superovulation promote changes in gene expression of 7 days old embryos that may be related to their developmental competence. These modifications are associated with downregulation of beta-estradiol pathway, upregulation of trophoblast-related genes and downregulation of WNT signalling pathway. Our results suggest a potential sensitivity of future embryos to follicular P4 levels but do not allow to conclude if the effect is from the oocyte, the oviduct, or the uterus response to P4.

2024-06-04 | GSE249344 | GEO

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