Ontology highlight
ABSTRACT:
PROVIDER: PRJNA480721 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.]
2011-11-22 | GSE33395 | GEO
Project description:Effect of the low phytic acid mutation on gene expression of developing seeds of M955, a low phytic acid barley genotype with >90% reduction in phytic acid in mature seeds. Expression analysis using the Barley1 GeneChip was performed on total RNA from developing seeds (7DAA) of M955 lpa and wt sib-selections. Sib-selections were from BC2 populations of M955 with Harrington as the recurrent parent. Material was grown in field trials in two years 2003 and 2004. In 2003 expression analysis was done from 2 lpa and 3 wt sib-selections, and in 2004 analysis was done from 2 lpa and 2 wt sib-selections. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, David Bowen. The equivalent experiment is BB22 at PLEXdb.] genotype: M955 LPA sib-selection - year: 2003(2-replications); genotype: M955 LPA sib-selection - year: 2004(2-replications); genotype: M955 WT sib-selection - year: 2003(3-replications); genotype: M955 WT sib-selection - year: 2004(2-replications)
2011-11-22 | E-GEOD-33395 | biostudies-arrayexpress
Project description:Co-polymer 1,2-epoxy-5-hexene and divinyl benzene with terminal oxirane group is synthesized for the first time. High density of hydrophilic groups (-COOH, -OH) enhances hydrophilicity through facile functionalization with Diethylene Triamine (DETA) and chloroacetic acid. COOH-functionalized mesoporous polymeric beads provide high surface area and porosity, superior hydrophilicity, solvent resistance and good bio-capability for enriching N-Linked glycopeptides. Sensitivity, selectivity, reusability and batch to batch reproducibility are tested using model glycoproteins (HRP, IgG and avidin) and analyzed by MALDI-TOF-MS. Furthermore, N-glycosylation sites in N-glycopeptides of characteristic glycoproteins are identified from digested human serum.
2023-07-20 | PXD027783 | Pride
Project description:DNA-protein interactions regulate critical biological processes. Identifying proteins that bind to specific, functional genomic loci is essential for understanding the underlying regulatory mechanisms on a molecular level. Here, we describe a novel co-binding-mediated protein profiling (CMPP) strategy to investigate the interactome of DNA G-quadruplexes (G4s) in cellular chromatin. CMPP involves cell-permeable, functionalized G4-ligand probes that bind endogenous G4s and subsequently crosslink to co-binding G4-interacting proteins in situ. We show the robustness of CMPP on proximity labelling of a G4 binding protein in vitro. Employing this approach in live cells, we identify hundreds of putative G4-interacting proteins from various functional classes. Next, we observe high G4 binding affinity and selectivity for several G4 interactors in vitro and confirm direct G4 interactions for one of the top candidates in chromatin. Our studies provide a chemical approach to map protein interactions of specific nucleic acid features in living cells.
2021-06-28 | GSE165124 | GEO
Project description:Selective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.
2020-06-30 | GSE150165 | GEO
Project description:The interactions between proteins and nucleic acids have a fundamental function in many biological processes well beyond nuclear gene transcription and include RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins binding individual mRNAs in mammalian cells has greatly been augmented by recent surveys, no systematic study on the native proteins of human cells differentially engaging various types of nucleic acids in a non sequence-specific manner has been reported. We designed an experimental approach to cover the non sequence-specific RNA and DNA binding space broadly, including methylation, and test for its ability to interact with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high confidence direct binders, 249 of which were devoid of previous experimental evidence for binding nucleic acids. We could assign 513 specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and to individual domains. The evolutionary conserved protein YB-1, previously associated with cancer and gene regulation, is shown to bind methylated cytosine preferentially conferring YB-1 a potential epigenetic function. Collectively, the dataset represents a rich resource of experimentally determined nucleic acid-specific binding proteins in humans and, indirectly, for other species. Identification of genomic YB-1 binding sites in HEK293 cells
2013-06-18 | E-GEOD-47539 | biostudies-arrayexpress
Project description:Current methods for intracellular protein analysis mostly require the separation of specific organelles or the change of intracellular environment. However, the functions of these proteins are determined by their native microenvironment as they usually form complexes with ions, nucleic acids, and other proteins. Thus, we have explored a method for in situ crosslinking and mapping of mitochondrial proteins in living cells. Poly(lactic-co-glycolic acid) (PLGA) nanoparticles are functionalized with dihexadecyldimethylammonium bromide (DDAB) to deliver protein crosslinkers into mitochondria. In situ crosslinked proteins are analyzed using mass spectrometry.
2023-05-26 | PXD035433 | Pride