Single-cell RNA-seq of out-of-thaw bone marrow-derived mesenchymal stromal cells (BM-MSCs)
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE338608 | GEO | 2026/07/14
REPOSITORIES: GEO
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Project description:In frozen dough baking technology, baker’s yeast Saccharomyces cerevisiae encounter freeze-thaw injury. After thawing, dramatically decrease in cell viability and fermentation activity is caused by freeze-thaw injury. The freezing period is critical factor in freeze-thaw injury, thus we focused and investigated time-dependent gene expression profiles in recovery process from freeze injury. First, changes in gene expression profiles in S. cerevisiae in recovery process from freeze-thaw injury were analyzed using a DNA microarray. The results showed the genes which were involved in homeostasis of metal ions were time-dependent up-regulated 2-fold or more in a series. Then we examined whether these genes were related to tolerance in freeze-thaw injury by using deletion strain. The results showed that deletion of MAC1, CTR1, and PCA1 genes which involved in copper ion transport exhibited freeze-thaw sensitivity in compared with wild type. These genes are involved in copper ion uptake to a cell under a copper deficiency condition or in copper ion homeostasis, suggesting that it may be related between freeze-thaw injury and copper ion transport. To determine the effect of supplementation of copper ion on cells after freeze-thaw treatment, cell viability, intracellular superoxide dismutase (SOD) activity, and intracellular levels of reactive oxygen species (ROS) were examined by various copper ion condition medium. The results showed that intracellular SOD activity was increased and intracellular levels of ROS were decreased by supplementation of copper ion, but there was no significant difference in cell viability. These results of the present study may suggest that copper ion concentration in yeast cell after freeze-thaw treatment is important to recovery from freeze-thaw injury due to redox control of intracellular levels of ROS, but copper ion did not directly affect cell viability.
2009-02-28 | GSE14942 | GEO
Project description:In frozen dough baking technology, bakerâs yeast Saccharomyces cerevisiae encounter freeze-thaw injury. After thawing, dramatically decrease in cell viability and fermentation activity is caused by freeze-thaw injury. The freezing period is critical factor in freeze-thaw injury, thus we focused and investigated time-dependent gene expression profiles in recovery process from freeze injury. First, changes in gene expression profiles in S. cerevisiae in recovery process from freeze-thaw injury were analyzed using a DNA microarray. The results showed the genes which were involved in homeostasis of metal ions were time-dependent up-regulated 2-fold or more in a series. Then we examined whether these genes were related to tolerance in freeze-thaw injury by using deletion strain. The results showed that deletion of MAC1, CTR1, and PCA1 genes which involved in copper ion transport exhibited freeze-thaw sensitivity in compared with wild type. These genes are involved in copper ion uptake to a cell under a copper deficiency condition or in copper ion homeostasis, suggesting that it may be related between freeze-thaw injury and copper ion transport. To determine the effect of supplementation of copper ion on cells after freeze-thaw treatment, cell viability, intracellular superoxide dismutase (SOD) activity, and intracellular levels of reactive oxygen species (ROS) were examined by various copper ion condition medium. The results showed that intracellular SOD activity was increased and intracellular levels of ROS were decreased by supplementation of copper ion, but there was no significant difference in cell viability. These results of the present study may suggest that copper ion concentration in yeast cell after freeze-thaw treatment is important to recovery from freeze-thaw injury due to redox control of intracellular levels of ROS, but copper ion did not directly affect cell viability. Experiment Overall Design: Total RNA was extracted from the stress-treated yeast cells by using a hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan). cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix userâs manual (Affymetrix, Santa Clara, USA). Biotinyated cRNA was fragmented and then used as a probe.Affimetrix Yeast Genome 2.0 arrays (Affymetrix) were used as DNA microarrays. All experiments were done in duplicate independently
2009-03-07 | E-GEOD-14942 | biostudies-arrayexpress
Project description:Using Normal Donor Blood, the effects of pre-freeze and thaw incubation time variables on the global gene expression signature and yield from RNA extracted using the PAXgene Blood RNA System
2017-09-22 | GSE81371 | GEO
Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury.
2009-08-31 | GSE15461 | GEO
Project description:Single-cell RNA-seq of out-of-thaw bone marrow-derived mesenchymal stromal cells (BM-MSCs)
| PRJNA1495244 | ENA
Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury. Total RNA was extracted from the stress-treated yeast cells by using a hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan). cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA). Biotinyated cRNA was fragmented and then used as a probe.Affimetrix Yeast Genome 2.0 arrays (Affymetrix) were used as DNA microarrays. All experiments were done in triplicate independently.
2009-08-31 | E-GEOD-15461 | biostudies-arrayexpress
Project description:Purpose: A Multiomics-based Unbiased Computational Modeling Platform Identifies Predictive Attributes of Mesenchymal Stromal Cell Immunomodulatory Potency Methods: scRNAseq from MSCs with dropseq method on BioRad ddseq platform Results: framework for identifying putative CQAs and generating MoA hypotheses for therapeutic cells and may help overcome current challenges in advancing large-scale, quality-driven manufacturing of cell therapies for broad clinical use. We used SureCell app to align the reads to human reference genome and used SEURAT for downstream analysis. Conclusions: Cell therapies are complex “living medicines” with potential to treat chronic, incurable diseases. Despite their success and promise, quality-driven reproducible manufacturing and identification of Mechanisms-of-Action (MoA) remain significant challenges. Specifically, it is difficult to identify which set of cell attributes, among the thousands of proteins, RNA, lipids, and metabolites, are most correlative to their function in a specific disease setting. Here, we report a multiomics-driven unbiased computational platform to identify multivariate features that are predictive of their immunomodulatory functions.
2025-12-02 | GSE195999 | GEO
Project description:Cryopreservation of human semen is widely used in assisted reproductive technology (ART) and male fertility preservation, but inevitably induces cryodamage to spermatozoa. Small non-coding RNAs, particularly microRNAs (miRNAs), play critical roles in post-transcriptional gene regulation and may reflect cellular responses to cryopreservation stress. Seminal plasma, the natural fluid environment of spermatozoa, contains abundant miRNAs that may also reflect post-thaw biological responses. However, the impact of freeze-thawing on miRNA expression in both sperm and seminal plasma remains poorly understood. In this study, we performed small RNA sequencing on sperm and seminal plasma samples from healthy normozoospermic donors. For sperm, 5 individual donors provided paired fresh and post-thaw samples (A1-A5: post-thaw; B1-B5: fresh). For seminal plasma, 30 donors were randomly divided into 3 groups (n=10 per group), pooled, and split into fresh control (D3, D4, D5) and cryopreservation-thawing (C3, C4, C5) groups. In sperm, cryopreservation-thawing induced [X] differentially expressed miRNAs ([Y] upregulated, [Z] downregulated). In seminal plasma, we identified 15 differentially expressed miRNAs (9 upregulated, 6 downregulated). GO and KEGG analyses revealed enrichment in fatty acid degradation, Toll-like receptor signaling, and oxidative phosphorylation pathways in both sample types. Our findings provide a comprehensive resource for understanding the molecular mechanisms of sperm cryodamage and developing biomarker-based tools for post-thaw semen quality assessment in ART settings.
2026-06-30 | GSE334372 | GEO
Project description:Bacterial community succession in permafrost thaw ponds
| PRJEB18072 | ENA