Ontology highlight
ABSTRACT:
PROVIDER: PRJNA791714 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Human breast milk (HBM) is the ideal source of nutrients for infants and is rich in microRNA (miRNA). In recent years, expressed breast milk feeding rather than direct breastfeeding is becoming increasingly prevalent for various reasons. HBM requires storage and processing, which can cause various changes in the ingredients. We investigated how the miRNAs in HBM change due to processes often used in real life. HBM samples collected from 10 participants were each divided into 7 groups according to the storage temperature, thawing method, and storage period. And we analyzed the miRNA changes in each group. Significant changes in expression of several miRNAs were confirmed when HBM were heated by microwave immediately after collection, stored at room temperature for 1 week, or frozen for 1 week. Changes in expression were also dependent on the frozen period or thawing method. However, there was no change in the miRNA expression in all samples refrigerated for 1 week. The expression of miRNA can change depending on the diverse processing, storage, and thawing methods of breast milk, and refrigerated storage may be an ideal method to maintain a state of miRNA.
2022-11-03 | GSE216940 | GEO
Project description:Deep RNA sequencing analysis revealed that compared to control (no cold storage/ischemia), 6h-cold storage led to 266 differentially expressed genes, many of which were implicated in modulating mitochondrial performance, oxidative stress response, myocardial function, and apoptosis. Either bone marrow- (BM) or adipose tissue-derived (Ad) mesencymal stromal cell conditioned medium (MSC-CM) restored these gene expression towards control.
2022-07-20 | GSE208341 | GEO
Project description:Human milk is highly recommended for infant during the first six month of life by World Healthy Organisation (WHO). Human milk is not only rich in macro-nutritional components, but also rich in cells and molecules. MicroRNAs are small non-coding RNAs, which enriched in human milk. These molecules are vital in enormous biological and cellular functions including immune system and in response to infections. By using deep sequencing method, 770,374,554 raw reads were generated from all samples (n=26). Then, filter analysis was done to remove 81,091,772 (10.5%), and 689,282,782 clean reads (89.5%) were considered as clean reads, which was retained for the subsequent bioinformatics analysis. Annotation and matching reads to miRBase revealed1780 mature known microRNAs identified in human milk cells and lipids derived from healthy, cold and other infection types mothers. In particular, 1680 known microRNAs were determined in infected mothers (n=14), while 1,606 known microRNAs in healthy mothers (n=12). Of these known microRNAs, 453 microRNAs were differentially expressed (p<0.05) between healthy and infected samples. The majority of the highly expressed miRNAs in all samples, in particular top 20 microRNAs, were also differentially expressed between healthy and infections. Further, 592 novel mature microRNA sequences were predicted, with only 65,878 total reads. Amongst the total reads of the novel microRNAs, top 20 novel miRNAs were found to contributed in 73.3% (total reads 48,295) of the total reads (65,878).
2017-12-22 | GSE80546 | GEO
Project description:Hepatic injury provoked by cold storage is a major problem affecting liver transplantation, as exposure to cold induces apoptosis in hepatic tissues. Long noncoding RNAs (lncRNAs) are increasingly understood to regulate apoptosis, but the contribution of lncRNAs to cold-induced liver injury remains unknown. Using RNA-seq, we determined the differential lncRNA expression profile in mouse livers after cold storage and found that expression of the lncRNA TUG1 was significantly down-regulated. Over-expression of TUG1 attenuated cold-induced apoptosis in mouse hepatocytes and liver sinusoidal endothelial cells LSECs, in part by blocking mitochondrial apoptosis and ER stress pathways. Moreover, TUG1 attenuated apoptosis, inflammation and oxidative stress in vivo in livers subjected to cold storage. Over-expression of TUG1 also improved hepatocyte function and prolonged hepatic graft survival rates in mice. These results suggest that the lncRNA TUG1 exerts a protective effect against cold-induced liver damage by inhibiting apoptosis in mice, and suggests a potential role for TUG1 as a target for the prevention of cold-induced liver damage in liver transplantation.
2016-01-07 | GSE76609 | GEO
Project description:A transcriptome analysis was applied on two peach (Prunus persica L.) cultivars with different sensitivity to low temperature regimes to identify cold-responsive genes that might be involved in tolerance to long low temperature storage. Peach fruit from ‘Morettini No2’ and ‘Royal Glory’, a sensitive and a tolerant, to chilling injury cultivars, respectively, were harvested at commercial maturity stage and allowed to ripen at room temperature (25°C) or subjected to 4 and 6-weeks of cold storage (0°C, 95% R.H.) followed by ripening at room temperature. Microarray experiments, employing the peach microarray platform (μ PEACH 1.0), were carried out by comparing harvested fruit against 4- and 6-week cold-stored fruit. The analysis identified 173 and 313 genes that were differentially expressed in ‘Morettini No2’ and ‘Royal Glory’ fruit after 4 weeks, respectively. However, the 6 weeks cold storage provoked a decrease in the total number of genes differentially expressed in both cultivars. RNA blot analysis validated the differential expression of certain genes showed in microarray data. Among these genes, two heat shock proteins (hsps), a putative β-D-xylosidase, an expansin, a dehydrin and a pathogenesis-related protein PR-4B precursor were induced during cold storage in both cultivars. The induction of hsps and the putative β-D-xylosidase appeared to be independent on the duration of postharvest treatment. On the other hand, transcript levels of lipoxygenase were quite constant during postharvest ripening, while a strong reduction or disappearance was observed after cold storage. A dehydration-induced RD22-like protein showed a reduction in the accumulation of transcripts during postharvest ripening independently on the temperature conditions. Overall, the current study shed some light on the molecular aspects of cold stress in peach fruit quality and identified some ripening and/or cold-induced genes which function need further elucidation.
2011-08-26 | GSE18280 | GEO
Project description:Tubers are vegetative reproduction organs formed from underground extensions of the plant stem. Potato tubers are harvested and stored for months. Storage under cold temperatures of 2 - 4 °C is advantageous for supressing sprouting and diseases. However, development of reducing sugars can occur with cold storage through a process called cold-induced sweetening (CIS). CIS is undesirable as it leads to darkened color with fry processing. The purpose of the current study was to find differences in biological responses in eight cultivars with variation in CIS resistance. Transcriptome sequencing was done on tubers before and after cold storage and three approaches were taken for gene expression analysis: 1. Gene expression correlated with end-point glucose after cold storage, 2. Gene expression correlated with increased glucose after cold storage (after-before), and 3. Differential gene expression before and after cold storage. Cultivars with high CIS resistance (low glucose after cold) were found to increase expression of an invertase inhibitor gene and genes involved in DNA replication and repair after cold storage. The cultivars with low CIS resistance (high glucose after cold) showed increased expression of genes involved in abiotic stress response, gene expression, protein turnover and the mitochondria. There was a small number of genes with similar expression patterns for all cultivars including genes involved in cell wall strengthening and phospholipases. It is proposed that the pattern of gene expression is related to chilling-induced DNA damage repair and cold acclimation and that genetic variation in these processes are related to CIS.
2019-11-14 | GSE138254 | GEO
Project description:Human milk, the best enteral selection for a preterm infant, becomes altered during freezing and soluble free fatty acid is generated over time. Free fatty acids may form complexes, such as the oleic acid-bound protein called HAMLET (human α‐lactalbumin made lethal to tumor cells). We determined the in vitro biological activity of preterm human milk protein‐oleic complexes (HAMLET-like complexes) and tested the hypothesis that laboratory-synthesized HAMLET exhibits cytotoxicity in human immature epithelial intestinal cell culture. Thirty-four milk samples from 15 mothers of hospitalized preterm infants were donated over time. Milk fractions were tested repeatedly for FHs 74 Int and HIEC-6 fetal cell cytotoxicity, using a sensitive viability assay. Protein and fatty acid identities were confirmed by Western blot, high performance liquid chromatography, and mass spectrometry. Cytotoxicity of intestinal cells exposed to milk increased respective to milk storage time (p<0.001) and was associated with free oleic acid (p=0.009). Synthesized HAMLET was cytotoxic in cultures of both lines. Preterm milk samples killed most cells in culture after an average 54 days in frozen storage (95% C.I. 34-72 days). After prolonged storage time, preterm milk and HAMLET showed a degree of cytotoxicity to immature intestinal cells in culture. Protein was reduced 221 in 1 mM dithiothreitol and alkylated in 5.5 mM
2022-08-12 | PXD034652 | Pride
Project description:To further explore the underlying mechanisms of the protection functions of human milk exosmes, high throughput sequencings were used to identify differentially expressed lncRNA and mRNA profiles between human milk exosomes form term human breast milk (Term-Exos) and preterm human breast milk (Pre-Exos).
2022-11-15 | GSE217708 | GEO