Ontology highlight
ABSTRACT:
PROVIDER: PRJNA943490 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23821529_1.fastq.gz | Fastqsanger.gz | |||
| SRR23821529_2.fastq.gz | Fastqsanger.gz | |||
| SRR23821530_1.fastq.gz | Fastqsanger.gz | |||
| SRR23821530_2.fastq.gz | Fastqsanger.gz | |||
| SRR23821531_1.fastq.gz | Fastqsanger.gz |
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Project description:Kinetics of spontaneously fermented vegetables
| PRJEB79031 | ENA
Project description:Certain neuron types fire spontaneously at high rates, an ability that is crucial for their function in brain circuits. The spontaneously active GABAergic neurons of the substantia nigra pars reticulata (SNr), a major output of the basal ganglia, provide tonic inhibition of downstream brain areas. A depolarizing "leak" current supports this firing pattern, but its molecular basis remains poorly understood. To understand how SNr neurons maintain tonic activity, we used single-cell RNA sequencing to determine the transcriptome of individual SNr neurons. We discovered that SNr neurons express the sodium leak current, NaLCN and that SNr neurons lacking NaLCN have impaired spontaneous firing.
2016-05-13 | GSE78521 | GEO
Project description:Certain neuron types fire spontaneously at high rates, an ability that is crucial for their function in brain circuits. The spontaneously active GABAergic neurons of the substantia nigra pars reticulata (SNr), a major output of the basal ganglia, provide tonic inhibition of downstream brain areas. A depolarizing "leak" current supports this firing pattern, but its molecular basis remains poorly understood. To understand how SNr neurons maintain tonic activity, we used single-cell RNA sequencing to determine the transcriptome of individual SNr neurons. We discovered that SNr neurons express the sodium leak current, NaLCN and that SNr neurons lacking NaLCN have impaired spontaneous firing. RNA sequencing profiles from 87 GFP-positive GABAergic SNr neurons and 9 GFP-negative SNr cells were carried out. However only 80 samples that passed initial quality control and that were included in the data processing are represented in this record.
2016-05-13 | E-GEOD-78521 | biostudies-arrayexpress
Project description:As an important adaptation to drought stress, several agronomic species, such as soybean and maize, can maintain the primary root substantial elongation rates at low water potentials, whereas shoot growth stops completely. In soybean, kinematic characterization of the spatial patterns of cell expansion within the root elongation zone showed that at low water potentials, elongation rates were preferentially maintained toward the root apex but were progressively inhibited at more basal locations, resulting in a shortened growth zone. To explore the molecular mechanism of root elongation in response to water stress, we set out to examine the expression of soybean genes in different root regions after 5 hours (5h) and 48 hours (48h) water stress treatment using the Affymetrix Soybean GeneChip containing 37,500 G. max probe sets.
2020-08-15 | GSE102749 | GEO
Project description:ABSTRACT: Background: Though central to our understanding of how roots perform their vital function of scavenging water and solutes from the soil, no direct genetic evidence currently exists to support the foundational model that suberin acts to form a chemical barrier limiting the extracellular, or apoplastic, transport of water and solutes in plant roots. Methodologies/Principle Findings: Using the newly characterized enhanced suberin1 (esb1) mutant, we established a connection in Arabidopsis thaliana between suberin in the root, and both water movement through the plant, and solute accumulation in the shoot. Esb1 mutants, characterized by increased root suberin, were found to have reduced day time transpiration rates, and increased water use efficiency during their vegetative growth period. Furthermore, these changes in suberin and water transport were associated with decreases in the accumulation of Ca, Mn and Zn, and increases in the accumulation of Na, S, K, As, Se and Mo in the shoot. Conclusions/Significance: Here we present direct genetic evidence establishing that suberin in the roots plays a critical role in controlling both water and mineral ion uptake and transport to the leaves. The changes observed in the elemental accumulation in leaves are also interpreted as evidence that a significant component of the radial root transport of Ca, Mn and Zn occurs in the apoplast. Keywords: genomic hybridization bulked segregant analysis
2009-04-14 | GSE15655 | GEO
Project description:Oral administration of an extract of compost fermented with thermophiles to pigs reduces the incidence of stillbirth and promotes piglet growth. However, the mechanism by which compost extract modulates the physiological conditions of the animals remains largely unknown. Here, we investigate the effects of compost extract on the gene expression in the intestine of the rat as a mammalian model. Gene expression analyses of the intestine indicated that several immune-related genes were upregulated following compost exposure. Thus, thermophile-fermented compost can contain microbes and/or substances that activate the gut mucosal immune response in the rat. In Male Wistar rats aged 3 weeks, tap water was supplemented with 1.0% (v/v) compost extract for the experimental rats, whereas water only was given to the control rats. The rats received water ad libitum for 12 weeks. Fresh gut samples were collected from individual rats at the end of the feeding test and stored at -80°C. The intestine were separated from the gut and used as samples for the isolation of total RNA. otal RNA was then subjected to microarray experiments using the Whole Rat Genome (4x44k) Oligo Microarray (Agilent Technologies, Inc.)
2012-11-02 | E-GEOD-37732 | biostudies-arrayexpress
Project description:affy_popsec_nancy_roots_poplar - This project aims to identify genes of interest for water deficit acclimation and/or adaptation in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices, in two genotypes, Carpaccio and Soligo, at various stages and intensities of stress. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit. The comparison between medium and severe stress intensities and between early and long term stresses will power the selection of genes of interest. The co-analysis of two genotypes of contrasted tolerance to water deficit should help to better discriminate genes presenting a potential adaptative character from genes responding passively to the constraint.-Two poplar clones, Soligo (S) and Carpacio (C) were submitted to 4 treatments: control, mild water deficit, moderate water deficit (12-day long for both) and early-drought stress (about 36-h long). Growth and physiology was characterised on a batch of plants and samples collected on another batch of plants. Four to eight root apices (1 cm-long) were collected on each individual tree. Total RNAs were extracted from all roots for each tree individually. Two pools of 3 (or 2) individuals were made using equimolar ratio. A pool is considered as one biological replicate and corresponds to one Affymetrix slide. The two biological replicates originate from the same experiment. Keywords: treated vs untreated comparison
2011-01-15 | GSE17223 | GEO
Project description:affy_popsec_nancy_pophydro_roots_poplar - This project aims to identify genes of interest for control of root growth in response to water deficit in a tree species: poplar. We look for genes and gene expression networks related to drought stress. We intend to analyse the transcriptome in root apices of cuttings grown in hydroponics and osmotically stressed with PEG. Root apex is the location of root elongation and these analyses intend to identify genes involved in the control of cell expansion and thus of root elongation. Indeed, root growth maintenance in response to water shortage contributes to plant tolerance to water deficit.-Poplar cuttings (cv Soligo) were grown in hydroponics. A moderate water deficit was applied by adding PEG to the nutrient solution (200g/l). After 3 days, the apex (1 cm-long) of the roots of each cutting were collected. For control and stressed treatments, RNAs were extracted from two pools of 5 to 9 roots (issued from 2 to 5 cuttings). A pool is considered as one biological replicate and corresponds to one Affymetrix slide. Keywords: treated vs untreated comparison
2011-01-15 | GSE17225 | GEO