Ontology highlight
ABSTRACT:
PROVIDER: PRJNA839273 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19264471.fastq.gz | Fastqsanger.gz | |||
| SRR19264472.fastq.gz | Fastqsanger.gz | |||
| SRR19264473.fastq.gz | Fastqsanger.gz | |||
| SRR19264474.fastq.gz | Fastqsanger.gz | |||
| SRR19264475.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Neoporphyra haitanensis Raw sequence reads
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Project description:Phycospheric and environmental microbes in Neoporphyra haitanensis during the cultivation cycle
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Project description:Colonization of land from marine environments was a major transition for biological life on Earth, and intertidal adaptation was a key evolutionary event in the transition from marine- to land-based lifestyles. Multicellular intertidal red algae exhibit the earliest, systematic, and successful adaptation to intertidal environments, with Porphyra sensu lato (Bangiales, Rhodophyta) being a typical example. We used proteomic analyse to reveal the complex regulation of rapid responses to intertidal dehydration/rehydration cycling within Neoporphyra haitanensis. These adaptations include rapid regulation of its photosynthetic system, a readily available capacity to utilize ribosomal stores, an excess of methylation supply to rapidly synthesize proteins, and a strong anti-oxidation system to dissipate excess redox energy upon exposure to air. These novel insights into the unique adaptations of red algae to intertidal lifestyles inform our understanding of adaptations to intertidal ecosystems and the unique evolutionary steps required for intertidal colonization by biological life.
2022-02-16 | PXD028649 | Pride
Project description:Purpose: Lactococcus lactis is the primary constituent of many industrial starter cultures used in food fermentations. However, this bacterium is exposed to several stressful conditions during the industrial process. L. lactis TOMSC161 has been shown to resist better to freeze-drying and storage when cells are harvested at the late stationary compared to the early stationary phase. Methods: In this work, the physiological changes that occur during growth (early and late stationary phases) were studied using transcriptomic, proteomic and cytometric approaches in order to elucidate the cell mechanisms involved in the stress tolerance of L. lactis TOMSC161 to freeze-drying and storage processes. Results: The majority of altered abundances for genes determined by transcriptomic analysis indicated a slowdown at the late stationary phase in general metabolism and in the incomplete reduction of O2 leading to reactive oxygen species (ROS), in comparison to the early stationary phase. Furthermore, the expression of genes involved in general and oxidative stress responses was over-expressed at the late stationary phase when compared to the early stationary phase, thus explaining the better resistance to freeze-drying and the storage of cells harvested after six hours of stationary phase. Superoxide anion detection was performed by flow cytometry and related to the ROS production of starters. Superoxide anion concentration was lower for cells harvested at the late stationary phase when compared to cells harvested at the early stationary phase. Conclusions: L. lactis TOMSC161 was thus able to develop an oxidative stress “pre-adaptation” during the stationary phase making it possible to better resist freeze-drying and storage stresses and especially oxidative stress.
2018-10-30 | GSE74554 | GEO
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:In this project, we report the detrimental effect of hydroxylamine, a quenching reagent for NHS-amine reaction, on phosphopeptides. The degree of phosphopeptide enrichment was greatly improved by a desalting method compared with a vacuum-drying method right after quenching reaction. We demonstrate that vacuum-drying in presence of hydroxylamine promotes β-elimination of phosphate groups from phosphoserine and phosphothreonine.
2018-02-27 | PXD008082 | Pride
Project description:<p>The Biospecimen Pre-analytical Variables (BPV) Program is a National Cancer Institute-sponsored study to systematically assess the effects of pre-analytical factors on the molecular profile of biospecimens. A robust biospecimen collection infrastructure was established to prospectively collect biospecimens using rigorous standard operating procedures to control for most variables while introducing experimental conditions to study specific biospecimen handling issues, including the cold ischemic time (delay to formalin fixation), time in formalin, freezing methods, and storage temperatures and durations. RNA and DNA from biospecimens collected under these conditions was analyzed on multiple molecular platforms. The potential effects of these pre-analytical conditions on protein integrity and detection of metabolites were also examined. Data from this study will be used to develop evidence-based biospecimen standard operating procedures and best practices for fit-for-purpose collection, processing, and storage of biospecimens.</p> <p>The BPV Cohort is utilized in the following dbGaP substudies. To view genotypes, analysis, expression data, other molecular data, and derived variables collected in these substudies, please click on the following sub-studies below or in the "Substudies" box located on the right hand side of this top-level study page phs001304 BPV Cohort. The substudy links will be active once they are released by dbGaP.</p> <p> <ol> <li>Preanalytical Impacts on Global Metabolite Profiling - plasma (MassSpec by Metabolon) This study was to evaluate the impact of the storage temperature (s) (-80°C and LN2 vapor) and the length of storage on human plasma quality using LC-MS/MS (liquid-chromatography-mass spectrometry/mass spectrometry) based global metabolite profiling. The study includes 240 plasma samples collected from 40 donors.</li> <li>Investigate the effect of the delay to fixation on the proteome and phosphoproteome -FFPE (MassSpec by Caprion). The study is to do proteome and phosphoproteome analysis on Delay to fixation was carried out using FFPE tumor samples from colon and ovarian cancer patients comparing 2, 3, and 12hr delay to fixation to the 1hr time point. The study includes 100 samples 20 donors.</li> <li>Investigate the effect of storage conditions of tumor specimens on the proteome and phosphoproteome profiling- Frozen tissue and plasma (MassSpec by Caprion). The study was to evaluate the effects of storage conditions on tumor specimens. Plasma samples from 40 cancer patients stored at two different temperatures (-80°C and LN2) for a given period (0-2, 6-8, and 12-14 months) were evaluated. Frozen kidney tumor samples from 20 patients were compared for effects of different snap frozen (dry ice vs. LN2) and storage temperatures (-80°C and LN2). The study includes 100 tissue and 240 plasma samples from 60 donors.</li> <li>Preanalytical Impacts on Genomic Sequencing by Next Generation Sequencing (NGS) technology (mRNA/miRNA and WES by Expression Analysis). The goal of the study is to determine the effects of cold ischemic delay-to-fixation (4 time points) and formalin preservation (FFPE) on the nature and quality of genomic profiles using the matched freshly frozen sample as the gold standard, which including WES, RNAseq. The study includes 395 samples from 37 donors.</li> <li>Preanalytical Impacts on Copy Number Variation (CNV) Detection by aCGH technology (aCGH by Georgetown University). This study was to use aCGH to evaluate the effect of variation in cold ischemia time and time in formalin fixation on CNV in DNA extracted from kidney cancer specimens. The study includes 235 samples from 40 donors.</li> <li>Evaluation of frozen conditions on mRNA profiling by TaqMan assay (mRNA expression by Georgetown University). This study was to utilize gene expression profiling, using custom TaqMan arrays, to compare the molecular profiles of RNA from frozen tumor samples collected using two freezing methods (dry ice or LN2), two storage temperatures (-80°C or LN2 vapor), as well as Optimal Cutting Temperature (OCT) compound and non-OCT embedded. The study includes 100 samples from 20 donors.</li> <li>mRNA signature for stratification by cold ischemia time (mRNA expression by IBBL). The study was to determine the effects of cold ischemic time (delay-to-fixation) and formalin preservation (FFPE) on mRNA detection by Taqman assay using tumor tissue specimens from kidney, colon and ovarian cancer patients. There are160 samples from 40 donors.</li> </ol> </p> <p><b>The Biospecimen PV cohort is utilized in the following dbGaP individual studies.</b> To view molecular data, and derived variables collected in these individual studies, please click on the following individual studies below or in the "Sub-studies" box located on the right hand side of this top-level study page <a href="study.cgi?study_id=phs001304">phs001304</a> Biospecimen PV cohort. <ul> <li><a href="study.cgi?study_id=phs001634">phs001634</a> CIT mRNA</li> <li><a href="study.cgi?study_id=phs001635">phs001635</a> CNV aCGH</li> <li><a href="study.cgi?study_id=phs001636">phs001636</a> Fixation Delay</li> <li><a href="study.cgi?study_id=phs001637">phs001637</a> Global Metabolite Profiling</li> <li><a href="study.cgi?study_id=phs001638">phs001638</a> mRNA TaqMan</li> <li><a href="study.cgi?study_id=phs001639">phs001639</a> NGS</li> <li><a href="study.cgi?study_id=phs001640">phs001640</a> Tumor Storage</li> </ul> </p>
| phs001304 | dbGaP