Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

15 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq data on leaf 8 blade tissue of 62 individual Brassica napus (Darmor) plants grown in the field.

ABSTRACT: 62 individual Brassica napus plants of the same accession grown in the same field were expression-profiled in autumn 2016 and phenotyped extensively until harvest in spring 2017. Machine learning models were used to link gene expression to the phenotypes of individual plants, with the purpose of assessing how much phenotype information in encoded in ‘noisy’ gene expression variation among individual plants of the same background grown under the same uncontrolled field conditions. Rosette leaf 8 blades of 62 individual Brassica napus plants of the same winter-type accession (BnASSYST-120, Darmor) grown in the same field (50°58'24.9\\"N 3°46'49.1\\"E, Merelbeke, Belgium) were RNA-seq profiled. No treatments or stresses were applied, all plants were profiled individually under uncontrolled field conditions. Sown at 2016-09-08, rosette leaf 8 sampled for RNA-seq at 2016-11-28, plants harvested at 2017-06-13.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Brassica napus

SUBMITTER: Sam De Meyer

PROVIDER: E-MTAB-11904 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Rice Lateral Root Inducible System timeseries

Project description:To transcriptionally characterize lateral root development in rice, we subjected the rice LRIS to genome-wide transcript profiling via RNA-sequencing. Taking into account the appearance of the first (stage I primordium) cell divisions starting from 6 hours after NAA treatment, we sampled at 2 hours and at 5 hours after NAA treatment to capture the primary auxin response and the gene expression related to initiation, respectively. Additionally, we sampled at 8 hours, 14 hours and 20 hours, in which the root was highly enriched for stage I, II and III primordia, respectively. As the spatiotemporal assessment of the primordia in the LRIS showed a highly synchronous induction and development of lateral roots in particular in the region just above the root meristem, root sections between 750 µm and 2000 µm from the root tip were microdissected and used for RNA-extraction. To assess possible artefacts induced by the replacement of the medium, we sampled a control before and 2 hours after replacement with NPA containing medium.

2023-08-24 | E-MTAB-13094 | biostudies-arrayexpress

Lateral root meristem establishment by LRIS in Arabidopsis

Project description:Previous transcript profiling of the Arabidopsis LRIS only occurred after 2 and 6 hours of NAA treatment (Himanen et al., 2004, Vanneste et al., 2005, De Smet et al., 2008). Here, we extended the time-course of the Arabidopsis LRIS to capture the expression during primordium formation. Therefore, we first characterized lateral root primordium development in the Arabidopsis LRIS, and performed staging in different regions of the root. We observed a slight loss of the synchronization in higher parts of the root. Nevertheless at 1 to 2 mm distance from the root tip, different stages of primordia were highly synchronously induced, and stage I, II and III primordia could be observed at 12, 18 and 24 hours after NAA treatment, respectively. We therefore sampled the 1 to 2 mm region from the root tip at 0, 12, 18 and 24 hours in the Arabidopsis LRIS, to sample stage I, II and III primordia, respectively.

2023-08-24 | E-MTAB-13112 | biostudies-arrayexpress

BRBseq performed on tumoroids and corresponding renal tumor tissues

Project description:To evaluate genetic similarities between tumoroids and the corresponding tumor tissues, we performed RNA sequencing of cells for each experimental condition. Since we injected human cancer cells into mice, cancer cells in the tumors were human while microenvironmental cells (i.e. Fibroblasts, Immune cells,…) were derived from mice. Thus, the RNA sequencing datasets generated from ACHN or 786-O tumor tissues (AxM and 7xM) and their respective tumoroids (AxTy and 7xTy) were mapped on human and mouse reference genome.

2023-06-30 | E-MTAB-12928 | biostudies-arrayexpress

RNAseq of the human gut commensal Bacteroides thetaiotaomicron wildtype, bt0700 and bt0700 bt3998 (ppGpp0) strains across three conditions: glucose minimal medium, 1h of carbon starvation, and mouse gut colonization

Project description:Transcriptional profiles of wildtype and mutant strains bt0700 and bt0700 bt3998 (ppGpp0) of human gut commensal B. thetaiotaomicron were collected to investigate the relevance of the stringent response mediated by the alarmone (p)ppGpp for growth and survival in three different conditions. RNAseq samples were taken during growth in glucose minimal medium, after 1h of carbon starvation, and after 6 days of monocolonizing germ-free mice (from cecum material).

2018-07-04 | E-MTAB-6412 | biostudies-arrayexpress

Adaptations to high pressure of Nautilia sp. strain PV-1, a piezophilic Epsilonproteobacterium isolated from a deep-sea hydrothermal vent

Project description:Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to those experienced in their natural habitat are critical to understand growth kinetics and metabolic adaptations to in situ conditions. The Epslilonproteobacterium, Nautilia sp. strain PV1, was isolated from hydrothermal fluids released from an active deep-sea hydrothermal vent at 9°N on the East Pacific Rise. Using a high pressure/high temperature continuous culture system we established that strain PV-1 has the shortest generation time of all known piezophilic microorganisms and we investigated its protein expression pattern in response to different hydrostatic pressures. Proteomic analyses of strain PV-1 grown at 200 Bars and 5 Bars showed that pressure adaptation is not restricted only to stress response or homeoviscous adaptation, but that it is more diversified and protein specific, with a fine and variegated regulation of enzymes involved even in the same metabolic pathway. As previously reported, proteins synthesis, motility, transport and energy metabolism are all affected by pressure, although to different extents. In strain PV-1, low pressure condition seems to activate the synthesis of phage-related proteins and an overexpression of enzymes involved in central carbon metabolism.

2023-05-10 | PXD022895 | Pride

Investigating impacts of mycothiazole and its synthetic derivative on mitochondrial function and aging in C. elegans

Project description:Small molecule inhibitors of mitochondrial electron transport chain (ETC) hold significant promise in the field of mitochondrial research and aging biology. In this study, we studied two molecules: mycothiazole (MTZ) - isolated from the marine sponge P. mycofijiensis and its semisynthetic acetylated derivative 8-O-acetylmycothiazole (8-OAc) as efficient alternatives for their high efficiency to inhibit ETC complex I function. Similar to rotenone, a widely used complex I inhibitor, these two compounds showed anticancer activity and strikingly demonstrate a lack of toxicity to non-cancer cells, a highly beneficial feature in the development of anti-cancer therapeutics. Furthermore, experiments with these small molecules in vivo utilizing C.elegans demonstrate their additional utilization to aging studies. We observed that both molecules have the ability to induce a mitochondria-specific unfolded protein response (UPRMT) pathway, which extends lifespan of worms when applied in their adult stage. Interestingly, we also found that these two molecules employ different pathways to extend lifespan in worms, where MTZ utilize the transcription factors, ATFS-1 and HSF-1, which are involved in the UPRMT and heat shock response (HSR) pathways, respectively. In opposition,8-OAc only required HSF-1 and not ATFS-1. This observation elucidates an important insight into the functional roles of various protein subunits of ETC complexes and their regulatory mechanisms associated with aging.

2024-01-01 | E-MTAB-13546 | biostudies-arrayexpress

Germinal Center B-Cell gene expression comparison between Wiskott-Aldrich syndrome protein KO mice and WT mice

Project description:This experiment intended to define differential gene expression between germinal center B cells expressing or not the Wiskott-Aldrich syndrome protein in mice. Sequencing was obtained on an Illumina HiSeq2500 system from Dark Zone GCB (DAPI-CD19+ GL7+IgD-CXCR4highCD86low) purified from CTL and GCBcWKO mice (n=4).

2021-06-01 | E-MTAB-10056 | biostudies-arrayexpress

RNA-seq of Pdx1-GFP+ sorted E10.5, wildtype and Hes1-/-. Neurog3-dependent Pancreas Dysgenesis Causes Ectopic Pancreas in Hes1 Mutants

Project description:RNA-seq of FACS Sorted E10.5 Pdx1-GFP+ of genotypes wildtype and Hes1-/-. Summary statement The developmental mechanisms that cause ectopic pancreas are poorly understood. We show that aberrant dorsal pancreas morphogenesis in Hes1 mutants leads to ectopic pancreas depending on the pro-endocrine gene Neurog3. Abstract Mutations in Hes1, a target gene of the Notch signalling pathway, lead to ectopic pancreas by a poorly described mechanism. Here we use genetic inactivation of Hes1 combined with lineage tracing in mouse embryos to reveal an endodermal requirement for Hes1 and that most ectopic pancreas tissue is derived from the E8.5 dorsal pancreas primordium. RNA-seq data from sorted E10.5 Pdx1-GFP+ cells from Hes1+/+ and Hes1−/− suggested that upregulation of endocrine lineage genes in Hes1−/− embryos was the major defect in the endoderm and accordingly early pancreas morphogenesis was normalised and the ectopic pancreas phenotype suppressed in Hes1−/−Neurog3−/− embryos. Analysis of other Notch pathway mutants uncovered a total depletion of progenitors in Mib1 deficient dorsal anlage, which was replaced by an anterior Gcg+ extension. Together, our results demonstrate that aberrant morphogenesis is the cause of ectopic pancreas and that a part of the endocrine differentiation program is mechanistically involved in the dysgenesis. Our results suggest that the ratio of endocrine lineage to progenitor cells is important for morphogenesis and that a strong endocrinogenic phenotype without complete progenitor depletion as seen in Hes1 mutants provokes an extreme dysgenesis that causes ectopic pancreas.

2018-08-20 | E-MTAB-6890 | biostudies-arrayexpress

RNA-seq of choroid and retina in tree shrews with choroidal neovascularization

Project description:In order elucidate the key signaling pathways in choroidal neovascularization, we induced choroidal angiogenesis by laser photocoagulation in 12 tree shrews and obtained mRNA profiles of their choroids and retinas by high-throughput transcriptome sequencing. Gene ontology(GO) and kyoto encyclopedia of genes and genomes(KEGG) enrichment analysis, hierarchical cluster analysis, weighted gene co-expression network analysis, protein-protein interaction (PPI) network analysis, and reverse transcription quantitative PCR (RT-qPCR) were performed.

2021-03-21 | E-MTAB-10198 | biostudies-arrayexpress

Retrograde signalling during caused by heritable mitochondrial dysfunction is partly mediated by ANAC017 and improves plant performance.

Project description:Mitochondria are crucial for plant viability and are able to communicate information on their functional status to the cellular nucleus via retrograde signalling, thereby affecting gene expression. It is currently unclear if retrograde signalling in response to constitutive mitochondrial biogenesis defects is mediated by the same pathways as those triggered during acute mitochondrial dysfunction. Furthermore, it is unknown if retrograde signalling can effectively improve plant performance when mitochondrial function is constitutively impaired. Here we show that retrograde signalling in mutants defective in mitochondrial proteins RNA polymerase rpotmp or prohibitin atphb3 can be suppressed by knocking out the transcription factor ANAC017. Genome-wide RNA-seq expression analysis revealed that ANAC017 is almost solely responsible for the most dramatic transcriptional changes common to rpotmp and atphb3 mutants, regulating both classical marker genes such as alternative oxidase 1a (AOX1a) and also previously-uncharacterised DUF295 genes that appear to be new retrograde markers. In contrast, ANAC017 does not regulate intra-mitochondrial gene expression or transcriptional changes unique to either rpotmp or atphb3 genotype, suggesting the existence of currently unknown signalling cascades. The data show that the role of ANAC017 extends beyond common retrograde transcriptional responses and affects downstream protein abundance and enzyme activity of alternative oxidase, as well as steady state energy metabolism in atphb3 plants. Furthermore, detailed growth analysis revealed that ANAC017-dependent retrograde signalling provides benefits for growth and productivity in plants with mitochondrial defects. In conclusion, ANAC017 plays a key role in both biogenic and operational mitochondrial retrograde signalling, and improves plant performance when mitochondrial function is constitutively impaired.

2016-07-28 | E-MTAB-4655 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data