Ontology highlight
ABSTRACT:
PROVIDER: PRJNA526939 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:En-route metabarcoding study of ballast water - comparative study of ballast water assessment using molecular apporaches (eDNA/eRNA metabarcoding and ATP tests)
| PRJEB25035 | ENA
Project description:We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity.
2014-07-24 | GSE49608 | GEO
Project description:Glioblastoma therapy relies on the alkylating drug temozolomide (TMZ) administered to irradiated patients post-neurosurgery, which increases overall survival but cannot prevent fatal disease relapse. Using clinical samples and glioblastoma models, we here identify TMZ-driven enrichment of ALDH1A1+ tumor subclones acquiring AKT-dependent drug resistance en route to relapse. We demonstrate that this recurrent phenotype switch is predictable and can be countered by a sequential rather than simultaneous combinatorial treatment approach.
2020-02-12 | GSE145128 | GEO
Project description:We performed whole-genome stability measurements for MDA-MB-231 and its highly metastatic derivative MDA-LM2. Our goal was to identify post-transcriptonal regulons that are deregulated en route to higher metastatic capacity. Cells were pulsed with 4-thiouridine for 2 hours and then RNA was extracted at 0, 2, 4, and 7 hr time-points in quadruplicate from each cell line. 4sU labeling followed by RNA-seq was then used to measure the abundance of transcripts in each population. A decay rate was estimated based on the rate at which transcript abundance was reduced at these time-points.
2014-07-24 | E-GEOD-49608 | biostudies-arrayexpress
Project description:We have used ATAC-seq to track cell state changes that occur during the differentiation of mouse embryonic stem cells to defined neural progenitor fates. We have performed ATAC-seq every 24 hours in cells en route to 3 distinct neural progenitors fates, anterior, hindbrain and spinal cord. This has allowed us to define how cells transition to a neural state, based on their enhancer usage. We identified regions distinct to different anterior-posterior neural progenitors, and validated their relevance by performing in vivo ATAC-seq on neural progenitors isolated from different axial levels of mouse embryos.
2018-08-27 | E-MTAB-6337 | biostudies-arrayexpress
Project description:Transcriptional analysis of the effects of natural environmental variation across the latitudinal range of Mytilus californianus Keywords: Environmental response
2008-03-26 | GSE8935 | GEO
Project description:Sensing environmental changes is important for survival of plants, as sessile organisms, in habi-tat. Recently, latitudinal clines in leaf senescence have been reported to be influenced by tem-perature and photoperiod. However, the relationship of light quality with latitudinal response of leaf senescence is still unclear. Here, we found that Arabidopsis accessions in far-red (FR) showed a strong negative correlation of leaf senescence with the latitude of their origin. phyto-chrome A (phyA) and B (phyB) mutants showed early and delayed senescence in FR, respec-tively, suggesting that PHYA and PHYB are involved in FR-dependent leaf senescence. Tran-scriptomic analysis identified genes oppositely regulated by PHYA and PHYB, and they were mainly associated with phytohormone, temperature, and defense, suggesting their associations with FR-dependent antagonistic effects of PHYA and PHYB on leaf senescence. Among these genes, the expression of WRKY6 in Arabidopsis accessions showed the highest correlation with latitude of their origin. Consistently, wrky6 mutant exhibited delayed senescence phenotype in FR. In conclusion, we propose that PHYs-regulated genes, including WRKY6, are involved in latitudinal leaf senescence in FR and this regulatory mode may contribute to latitudinal adapta-tion by responding FR, as a piece of geographical information.
2018-09-30 | GSE103946 | GEO
Project description:Understanding and quantifying the effects of environmental factors influencing the variation of abundance and diversity of microbial communities was a key theme of ecology. For microbial communities, there were two factors proposed in explaining the variation in current theory, which were contemporary environmental heterogeneity and historical events. Here, we report a study to profile soil microbial structure, which infers functional roles of microbial communities, along the latitudinal gradient from the north to the south in China mainland, aiming to explore potential microbial responses to external condition, especially for global climate changes via a strategy of space-for-time substitution. Using a microarray-based metagenomics tool named GeoChip 5.0, we showed that microbial communities were distinct for most but not all of the sites. Using substantial statistical analyses, exploring the dominant factor in influencing the soil microbial communities along the latitudinal gradient. Substantial variations were apparent in nutrient cycling genes, but they were in line with the functional roles of these genes. 300 samples were collected from 30 sites along the latitudinal gradient, with 10 replicates in every site
2015-05-23 | E-GEOD-69171 | biostudies-arrayexpress
Project description:A prospective, longitudinal analysis of the developing gut microbiome in infants en route to type 1 diabetes
| PRJNA231909 | ENA
Project description:Chemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95 % of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa-5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20-100x) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
2024-03-15 | PXD042549 | Pride