SOB4ESSwissComp
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB92381 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:au07-05_groundworms - groundworms - Do earthworms affect plant growth through signal molecules? - Plants were grown in a sandy soil from the Centre de Recherche en Ecologie Expérimentale et Prédictive (CEREEP, France), in the presence or absence of earthworms. Soil was dried and sieved at 2 mm before to be put in the pots. There was 2 levels of treatment (presence or absence of earthworms in the soil), and 5 plants per treatments. Keywords: treated vs untreated comparison
2010-10-01 | GSE24393 | GEO
Project description:au07-05_groundworms - groundworms - Do earthworms affect plant growth through signal molecules? - Plants were grown in a sandy soil from the Centre de Recherche en Ecologie Expérimentale et Prédictive (CEREEP, France), in the presence or absence of earthworms. Soil was dried and sieved at 2 mm before to be put in the pots. There was 2 levels of treatment (presence or absence of earthworms in the soil), and 5 plants per treatments. Keywords: treated vs untreated comparison 4 dye-swap - CATMA arrays
2010-09-30 | E-GEOD-24393 | biostudies-arrayexpress
Project description:We used quantitative RNA expression profiling on the Affymetrix U133 human expression array to validate quantitative expression results obtained with the tissue preservative RNALater against snap frozen and fresh tissues as a means of routine tissue collection and temporary storage. By using split samples from a homogenous tissue (uterine myometrium), and including duplicates within each processing group compared, we were able to undertake a formal ANOVA analysis comparing the magnitude of result variation contributed by sample source (different patients), processing protocol (fresh vs. frozen vs. 24 or 72 hours RNALater), and random background (duplicates). The dataset was randomly permuted to define a baseline pattern of test statistic values against which the observed results could be interpreted. Ambient storage of tissues for 24 or 72 hours in RNALater did not contribute any systematic shift in quantitative RNA expression results relative to the alternatives of fresh or frozen tissue. Keywords: parallel sample
2004-04-09 | GSE1296 | GEO
Project description:<p><strong>BACKGROUND:</strong> Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at - 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practical, however no available methodologies adequately preserve the metabolomic profile of stool. A novel sampling kit (OMNImet.GUT; DNA Genotek, Inc.) was introduced for ambient temperature storage and stabilization of feces for metabolomics; we aimed to test the performance of this kit vs flash-freezing. To do this stool was collected from an infant's diaper was divided into 2 aliquots: 1) flash-frozen and 2) stored in an OMNImet.GUT tube at ambient temperature for 3-4 days. Samples from the same infant were collected at 2 different timepoints to assess metabolite changes over time. Subsequently, all samples underwent metabolomic analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS).</p><p><strong>RESULTS:</strong> Paired fecal samples (flash-frozen and ambient temperature) from 16 infants were collected at 2 timepoints (32 individual samples, 64 aliquots). Similar numbers of metabolites were detected in both the frozen and ambient temperature samples (1126 in frozen, 1107 in ambient temperature, 1064 shared between sample types). Metabolite abundances were strongly correlated between storage methods (median Spearman correlation Rs = 0.785 across metabolites). Hierarchical clustering analysis and principal component analysis showed that samples from the same individuals at a given timepoint clustered closely, regardless of the storage method. Repeat samples from the same individual were compared by paired t-test, separately for the frozen and OMNImet.GUT. The number of metabolites in each biochemical class that significantly changed (p < 0.05) at timepoint 2 relative to timepoint 1 was similar in flash-frozen vs ambient temperature storage. Changes in microbiota modified metabolites over time were also consistent across both methodologies.</p><p><strong>CONCLUSION:</strong> Ambient temperature storage and stabilization of stool in the OMNImet.GUT device yielded comparable metabolomic results to flash freezing in terms of 1) the identity and abundance of detected biochemicals 2) the distinct metabolomic profiles of subjects and 3) changes in metabolites over time that are plausibly microbiota-induced. This method potentially provides a more convenient, less expensive home collection and storage option for stool metabolomic analysis.</p>
2021-01-27 | MTBLS201 | MetaboLights
Project description:ra04-07_pgpr - trancriptional response to 3 rhizobacteria - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. - Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sawn on agar mineral medium. Four days after storage in the dark at 4degreeC, seedlings were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on soil inoculated or not with 108 cfu.g-1 of Mesorhizobium loti, or 108 cfu.g-1 of Phyllobacterium STM196, or 107 cfu.g-1 of Bradyrhizobium ORS278. Keywords: treated vs untreated comparison
2007-06-20 | GSE7992 | GEO
Project description:Purpose: Recombinant human erythropoietin administration studies involving “omics” approaches have demonstrated a gene-expression signature that could aid detection of blood doping. However, current anti-doping testing does not involve blood collection into tubes with RNA preservative. This study investigated if whole blood in short-term storage could be used for transcriptomic analysis despite lacking RNA preservation. Methods: Whole blood samples were collected from fourteen male healthy individuals. Short-term storage: whole blood collected into K2EDTA tubes and subjected to short-term (i.e., at 4°C) storage for 6 hours, 12 hours, 24 hours and 48 hours. After storage, blood from K2EDTA tubes were transferred into Tempus™ Blood tubes, and then extracted using Tempus™ Spin RNA Isolation Kit (Life Technologies, Carlsbad, CA, USA). Samples from four subjects of each time point that presented higher RIN value (≥7) were selected for RNA_Seq analysis. Results: The experiment provided RNA quality and purity for gene expression analysis. Considering 6-hours storage as a reference group, the number of differentially expressed genes were 19, 45 and 70 in comparison to 12, 24 and 48-hours, respectively (which means 0.37, 0.88 and 1.37% of mapped genes). Of the 19 differentially expressed genes in the comparison 6 vs. 12-hours, 9 overlapped with the 45 in the comparison 12 vs. 24-hours. Furthermore, 40 of those 45 overlapped with the 70 differentially expressed in the comparison 6 vs. 48-hours. None of the transcripts described in previous studies (Durussel et al. 2016; Wang, Durussel, et al. 2017) were differently expressed. Conclusion: RNA quantity, purity and integrity was not significantly compromised from short-term storage in blood storage tubes lacking RNA stabilisation, indicating that transcriptomic/omics analysis could be conducted using anti-doping samples collected without RNA preservation.
2021-09-03 | GSE183132 | GEO
Project description:ra04-07_pgpr - profiling of the pgpr induced systemic resistance (isr) - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. - Seeds were sawn on 0.8% (W/V) agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on soil inoculated or not with 107 cfu.g-1 of Bradyrhizobium strain ORS278. Three weeks later, 3 leaves per plant were infiltrated with a suspension of Pseudomonas syringae pv. tomato (2.105 cfu.ml-1) or with MgSO4 10 mM alone for control plants. Infiltrated leaves were collected 24h later. Keywords: normal vs rnai mutant comparaison,treated vs untreated comparison
2007-06-20 | GSE7990 | GEO
Project description:Russet Nugget and the corresponding smooth skin mutant tubers harvested from disease and healthy filed plots. Tubers were washed with 10% Clorox and dried before harvesting tissue. Cortex and peel tissue was collected from healthy and infected regions of the mutant. Healthy peel and cortex tissue was collected from Russet Nugget (wild-type) potato tuber and snap-frozen in liquid nitrogen and stored at -80 °C. RNA was extracted from frozen tissues using a hot phenol method in triplicate from the different sets of tuber tissue. Extracted RNA was purified by Qiagen kits after treatment with DNAse. In all of these experiments RNA from Russet Nugget peel and cortex tissue will be used as reference samples where as mutant tissue will be used as query samples. Keywords: Direct comparison
2008-02-13 | GSE10485 | 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:ra04-07_pgpr - profiling of the root architecture response to phyllobacterium - Experiment 1 : Which genes are up- or down-regulated in Arabidopsis thaliana cultivated in vitro with increased lateral root development in response to Phyllobacterium STM196 inoculation. Experiment 2 : Which genes are up- or down-regulated during the ISR triggered by a rhizobacteria, in comparison with those affected by a pathogenic interaction. Experiment 3 : which genes are specifically induced or repressed in Arabidopsis thaliana by inoculation of the soil with a PGPR vs a bacteria that has the ability to trigger nodule formation in a Legume. - Seeds of wild-type Arabidopsis thaliana (ecotype Columbia) were surface-sterilized and sawn on agar mineral medium (see below). 4 days after storage in the dark at 4degreeC, seedling were cultivated 6 days in a growth chamber (16 h daily, 20-22degreeC) and then transferred on a fresh agar mineral medium inoculated or not with Phyllobacterium STM196 (2.108 cfu/ml). 6 days later, root and leaves were collected, froze on liquid nitrogen and stored at -80degreeC. Keywords: treated vs untreated comparison
2007-06-20 | GSE7991 | GEO