Asparagales
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1107706 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28956800_1.fastq.gz | Fastqsanger.gz | |||
| SRR28956800_2.fastq.gz | Fastqsanger.gz | |||
| SRR28956801_1.fastq.gz | Fastqsanger.gz | |||
| SRR28956801_2.fastq.gz | Fastqsanger.gz | |||
| SRR28956802_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 96 |
Similar Datasets
Project description:Transcriptome sequencing of human hepatocellular carcinoma
2025-01-24 | E-GEOD-33294 | ExpressionAtlas
Project description:Growth conditions influence growth rate and the corresponding global proteome composition. It is commonly observed that a higher ribosomal content due to growth rate optimization may impact the level of metabolic proteins. In the case of Lactococcus cremoris, acidification and flavor formation are important traits of their use in cheesemaking. This study correlates the expression level of metabolic (e.g., flavor-relevant) enzymes in relation to the level of ribosomes during growth in defined medium or milk.
2025-02-17 | PXD042113 | Pride
Project description:Flahaut2013 - Genome-scale metabolic model of L.lactis (MG1363)
Genome-scale metabolic model for Lactococcus lactis
MG1363 and its application to the analysis of flavor formation.
This model is described in the article:
Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation.
Flahaut NA, Wiersma A, van de Bunt B, Martens DE, Schaap PJ, Sijtsma L, Dos Santos VA, de Vos WM
Applied Microbiology and Biotechnology. 2013; 97(19):8729-8739
Abstract:
Lactococcus lactis subsp. cremoris MG1363 is a paradigm strain for lactococci used in industrial dairy fermentations. However, despite of its importance for process development, no genome-scale metabolic model has been reported thus far. Moreover, current models for other lactococci only focus on growth and sugar degradation. A metabolic model that includes nitrogen metabolism and flavor-forming pathways is instrumental for the understanding and designing new industrial applications of these lactic acid bacteria. A genome-scale, constraint-based model of the metabolism and transport in L. lactis MG1363, accounting for 518 genes, 754 reactions, and 650 metabolites, was developed and experimentally validated. Fifty-nine reactions are directly or indirectly involved in flavor formation. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the whole metabolic network. Anaerobic carbon-limited continuous cultures were used for estimating the energetic parameters. A thorough model-driven analysis showing a highly flexible nitrogen metabolism, e.g., branched-chain amino acid catabolism which coupled with the redox balance, is pivotal for the prediction of the formation of different flavor compounds. Furthermore, the model predicted the formation of volatile sulfur compounds as a result of the fermentation. These products were subsequently identified in the experimental fermentations carried out. Thus, the genome-scale metabolic model couples the carbon and nitrogen metabolism in L. lactis MG1363 with complete known catabolic pathways leading to flavor formation. The model provided valuable insights into the metabolic networks underlying flavor formation and has the potential to contribute to new developments in dairy industries and cheese-flavor research.
This model is hosted on BioModels Database
and identified by: MODEL1310300000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2005-01-01 | MODEL1310300000 | BioModels
Project description:Russeting of apple fruit is a non-invasive physiological disorder. It occurs mainly in 'Golden Delicious' apple and its hybrids, while understanding of its molecular mechanism is still limited. In this study, we used mRNA sequencing and an isobaric tag for relative and absolute quantitation-based quantitative (iTRAQ) proteomic analysis to detect changes in the expression levels of genes and proteins during russeting formation in russeted and non-russeted skin of 'Golden Delicious' apple. We set up three comparison groups representing the three developmental stages in the russeting formation process. With the formation of fruit russeting, there were 2856 differentially expressed genes and 942 differentially expressed proteins in the comparison groups as detected at the transcript level and protein level, respectively. A correlation analysis of the transcriptome and proteome data revealed related-genes involved in lignin biosynthesis are significant changes at different developmental stages during apple russeting formation. Some other transcription factors, such as MYBs, NACs and LIMs were also involved in apple russeting formation. In this study, one LIM transcription factor was preliminarily determined to be involved in lignin biosynthesis by combining to PAL-box element. Studying the identified genes and proteins will provide further insights into the molecular mechanisms controlling apple russeting formation.
2019-09-26 | PXD014960 | Pride
Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses.
2012-01-15 | GSE28159 | GEO
Project description:The human skeletal muscle transcriptome assessed with RNA sequencing
2025-01-21 | E-GEOD-58608 | ExpressionAtlas
Project description:We proposed that DNA recombination/repair processes play a role in memory formation. Here, we used microarray analysis of rat amygdala genes to identify possible DNA recombination/repair factors involved in memory consolidation of conditioned taste aversion (CTA). Among the genes that showed statistically significant differential expression, we identified fen-1, encoding a flap-structure specific DNA endonuclease. Amygdalar fen-1 mRNA induction was associated to the illness component of CTA, since it could be observed by the pairing of a flavor and gastrointestinal illness, by the illness itself, but not by the presentation of the flavor alone. No CTA related induction of fen-1 expression was observed in the insular cortex. Importantly, functional validation studies demonstrated that amygdalar suppression of fen-1 expression impaired memory consolidation of CTA. Overall, our studies helped identify a new DNA recombination/repair candidate factor involved in memory formation of aversive experiences. Two comparisons were established between the cRNA samples: CTA versus Flavor-only and CTA versus Toxin-only. For each comparison, the microarray experiment was repeated four times using new biological samples, each consisting of a sample pool from 3 animals. Two of the four biological replicates were performed as dye-swaps in order to correct for dye bias effects.
2009-12-30 | E-GEOD-11520 | biostudies-arrayexpress
Project description:Transcription profiling by high throughput sequencing of soybean transcriptome data
2019-05-15 | E-MTAB-4270 | ExpressionAtlas
Project description:Transcriptome sequencing of Foxtail millet Setaria italica for different tissues
2019-05-15 | E-GEOD-36391 | ExpressionAtlas
Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur.
2013-10-01 | GSE51289 | GEO