Neochloris oleoabundans RNA sequencing of 5 growth conditions, 8 samples
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500, Turbidostat
ORGANISM(S): Neochloris oleoabundans
SUBMITTER: Benoit Carreres
PROVIDER: E-MTAB-3651 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-10-10 | E-GEOD-46070 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE27245: Expression data from Top2β KO cells as well ICRF-193 treatment of in vitro derived neurons and cortical glutamatergic neurons GSE27246: Top2β ChIP-chip Refer to individual Series
2012-05-01 | E-GEOD-27247 | biostudies-arrayexpress
Project description:The cuticles of arthropods, including aquatic crustaceans like Daphnia, provide an interface between the organism and its environment. Thus, the cuticle’s structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the molted cuticle of Daphnia magna, which has long been a prominent subject of studies on ecology, evolution, and developmental biology, anddetected 278 high confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin modifying enzymes as most abundant protein groups in the cuticle proteome.Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the Daphnia cuticle . Finally, cuticle protein genes were clustered as tandem gene arrays in the Daphnia genome, indicating their importance for adaptation to environmental change. The cuticle proteome presented here will be a valuable resource to the Daphnia research community, informing investigations on diverse topics such as the genetic basis of interactions with predators and parasites.
2024-09-02 | PXD040228 | Pride
Project description:Here we compared the proteomes of microsomal fractions from primary tumors isolated from PyMT mice versus PyMTxCyp2c44-/- mice.
2020-03-03 | PXD017303 | Pride
Project description:The use of cell factories to convert sugars from lignocellulosic biomass into chemicals in which oleochemicals and food additives, such as carotenoids, play an important role is essential for the shift towards sustainable processes. Rhodotorula toruloides is a yeast that naturally metabolises a wide range of substrates, including lignocellulosic hydrolysates, and converts them into lipids and carotenoids. In this study, xylose, the main component of hemicellulose, was used as the sole substrate for R. toruloides, and a detailed physiology characterisation combined with absolute proteomics and genome-scale metabolic models was carried out to understand the regulation of lipid and carotenoid production. To improve these productions, oxidative stress was induced by hydrogen peroxide and light irradiation and further enhanced by adaptive laboratory evolution. Based on the online measurements of growth and CO2 excretion, three distinct growth phases were identified during batch cultivations. The intracellular flux estimations correlated well with the measured protein levels and demonstrated improved NADPH regeneration and phosphoketolase activity and reduced beta-oxidation, correlating with increasing lipid yields. Light irradiation conditions resulted in 70% higher carotenoid and 40% higher lipid yields. The presence of hydrogen peroxide did not affect the carotenoid yield but culminated in the highest lipid yield of 0.65 ± 0.06 g/gDCW. The adapted strain showed improved fitness and 130% higher carotenoid yield than the parental strain. This work presented a holistic view of xylose conversion into microbial oil and carotenoids by R. toruloides for further cost-effective and renewable production of these molecules.
2020-07-29 | PXD019305 | Pride
Project description:We tested the inhibitory effects of hydroalcoholic extracts from grape leaves in breast cancer malignancy using MCF-7 and SKBR-3 cell lines.
2020-05-27 | PXD016748 | Pride
Project description:Topoisomerases are essential for resolving topological problems in the genome, while their function in gene regulation, especially during cellular differentiation, remains unknown. We reveal that the expression of two Topo II isoforms, Top2a and Top2ß, is characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, Top2a preferentially binds to promoters embedded in an active chromatin environment. Inhibition of Top2a activity results in misregulation of target gene expression that accompanies accumulation of double-strand breaks. Common targets of Top2a and Top2ß are housekeeping genes while their unique targets are involved in proliferation/pluripotency and neurogenesis, respectively. Moreover, a subset of Top2a targets exhibit bivalent chromatin state that is resolved upon differentiation concomitant with their activation and occupancy by Top2ß, a feature further observed for long genes. These findings suggest that Top2a not only contributes to stem cell transcriptome regulation but may also prime developmental genes for subsequent activation upon differentiation. mRNA profiles of DMSO and ICRF-193 treated mESCs were generated by deep sequencing in triplicates. ICRF-193 is a well established catalytic inhibitor of Topoisomerase II, hence, we used ICRF-193 to the elucidate role of Top2a catalytic activity on transcription by genome wide transcription profiling.
2013-10-10 | E-GEOD-46066 | biostudies-arrayexpress
Project description:Topoisomerases are essential for resolving topological problems in the genome, while their function in gene regulation, especially during cellular differentiation, remains unknown. We reveal that the expression of two Topo II isoforms, Top2a and Top2ß, is characteristic of dividing and postmitotic tissues, respectively. In embryonic stem cells, Top2a preferentially binds to promoters embedded in an active chromatin environment. Inhibition of Top2a activity results in misregulation of target gene expression that accompanies accumulation of double-strand breaks. Common targets of Top2a and Top2ß are housekeeping genes while their unique targets are involved in proliferation/pluripotency and neurogenesis, respectively. Moreover, a subset of Top2a targets exhibit bivalent chromatin state that is resolved upon differentiation concomitant with their activation and occupancy by Top2ß, a feature further observed for long genes. These findings suggest that Top2a not only contributes to stem cell transcriptome regulation but may also prime developmental genes for subsequent activation upon differentiation. mRNA profiles of DMSO and ICRF-193 treated mESCs were generated by deep sequencing in triplicates. ICRF-193 is a well established catalytic inhibitor of Topoisomerase II, hence, we used ICRF-193 to the elucidate role of Top2a catalytic activity on transcription by genome wide transcription profiling.
2013-10-10 | E-GEOD-49141 | biostudies-arrayexpress
Project description:Here we undertook a proteomic investigation of ascending aorta from New Zealand White rabbits after 10 weeks on a high (2% w/w) cholesterol diet (HCD, n=5) or control diet (n=5) in order to profile the proteomic changes in response to the HCD. Histology confirmed intimal thickening in the HCD group and LC-MS/MS analysis of individually obtained ascending aorta extracts labelled with isobaric (iTRAQ) tags led to identification and quantitation of 453 unique proteins above the 1% false discovery rate threshold. Of 67 proteins showing significant differences in relative abundance (p<0.05), 62 were elevated and five decreased in ascending aorta from HCD-fed rabbits compared to controls. Six proteins were selected for validation using Multiple Reaction Monitoring which confirmed the iTRAQ results.
2018-06-21 | PXD002345 | Pride
Project description:Lipid nanoparticles (LNPs) play a crucial role in addressing genetic disorders, and cancer, and combating pandemics such as COVID-19 and its variants. Yet, in contrast remarkable achievements in siRNA and mRNA delivery, the ability of LNPs to effectively encapsulate large-size DNA molecules remains elusive. This is a significant limitation, as the successful delivery of large-size DNA holds immense potential for gene therapy, offering transformative opportunities for the treatment of a wide range of genetic diseases. To address this gap, the present study focuses on the design of PEGylated LNPs, incorporating large-sized DNA, and cationic lipids departing from traditional RNA and ionizable lipids. The resultant LNPs demonstrate a unique particle morphology characterized by distinct layered subunits composed of alternating lipid bilayers and DNA monolayers. Inspired by the ability of DNA to neutralize cationic lipids and promote the formation of an opsonin-deficient protein corona, these particles were further engineered after initial synthesis with a DNA coating and plasma proteins. This novel multicomponent bionanoconstruct exhibits enhanced transfection efficiency and safety in controlled laboratory settings and improved immune system evasion in in vivo tests. This capacity is attributed to its superior ability to evade lysosomal degradation and immune cell capture, a phenomenon that is mediated by a complex interplay among PEGylation, the protein corona, and DNA within the structure. These findings provide valuable insights for the design and development of bionanoarchitectures for large-size DNA delivery, opening new avenues for transformative gene therapies
2024-10-02 | PXD054751 | Pride