Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Selective TiO2-based enrichment methods for analyzing phosphopeptide content of small-size complex samples

ABSTRACT: Comparison of several TiO2-based phosphopeptide enrichment methods

INSTRUMENT(S): maXis

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Cervix Carcinoma

SUBMITTER: Gábor Tóth

LAB HEAD: Laszlo Drahos

PROVIDER: PXD019439 | Pride | 2020-12-17

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Vicia narbonensis (legume) and Pisum sativum (pea) expressing a bacterial phosphoenol pyruvate carboxylase during seed maturation

Project description:In order to change assimilate partitioning during seed maturation a bacterial phosphoenolpyruvate carboxylase (PEPC) has been expressed in V. narbonensis under control of the LegB4 promoter. Transgenic bean seeds accumulate app. 20% more protein and have higher seed weight. Physiological and biochemical analyses indicate a shift of metabolic fluxes from sugars/starch to organic acids/free amino acids suggesting increased anaplerotic carbon flow. This indicates that the availability of carbon acceptors limits seed protein synthesis. Gene expression was analysed in growing embryos using macro-arrays containing 5,548 seed-specific pea genes. Radioactive labeled cDNA probes were prepared from RNA isolated from embryo of developing seeds of wild type and transgenic PEPC plants of V. narbonensis (15, 17, 19, 21, 25, and 30 DAP) and hybridized to cDNA macroarrays.

2007-11-14 | E-IPKG-2 | biostudies-arrayexpress

Transcription profiling of pea seed development

Project description:SnRK1 (sucrose-non-fermenting-1-related) protein kinases are involved in the regulation of plant metabolism controlling both gene expression and phosphorylation. The aim of the study was to investigate the role of SnRK1 in pea seed development. To study the effect of SnRK1 deficiency, transgenic pea plants were generated carrying a gene for VfSnRK1 in antisense orientation under control of seed specific vicilin promoter. Selected transgenic lines were characterized with decreased levels of PsSnRK1 mRNA and reduced up to 71% phosphorylation activity. Antisense inhibition of SnRK1 resulted in reduced seeds fresh weight, defect of pollen development. To dissect the SnRK1-antisense phenotype at the molecular level, a search for genes with differential expression patterns in transgenic plant versus wild type seeds has been performed using cDNA macroarray analysis. Radioactive labeled cDNA probes were prepared from RNA isolated from embryo of developing seeds of wild type (11, 13, 15, 17, 19, and 21 DAP) and transgenic SnRK1-antisense plant (13, 15, 17 and 19 DAP), which correspond to the transition phase of seed development, and hybridized to cDNA macroarrays.

2013-01-30 | E-IPKG-1 | biostudies-arrayexpress

Sequencing of methylated GATC DNA fragments (Targeted DamID) from seven olfactory neuron populations in Drosophila melanogaster

Project description:This project’s aim was to compare the transcriptional profiles of olfactory sensory neurons in Drosophila melanogaster in order to identify novel genes that specify neuron-specific functions/phenotypes or may otherwise be involved in the development of the olfactory system. The isolation of sufficient numbers of intact olfactory sensory neurons (OSN) from the antenna of Drosophila melanogaster has so far limited single-cell transcriptomic approaches being applied to the adult fly antenna. Targeted DamID (TaDa) provides an alternative approach for profiling transcriptional activity in a cell-specific manor that bypasses the need for isolating OSN. Using the Gal4/UAS system, we applied TaDa to seven OSN populations and compared differences in Pol II occupancy for genes across these datasets.

2021-03-17 | E-MTAB-8935 | biostudies-arrayexpress

Transcription profiling of prostates from normal and Pten knock-out mice, and comparing the gene expression profile in the proximal and distal part of normal prostates

Project description:1. Comparison of gene expression profiles of normal prostates and prostates isolated from 4-5 months old PSA-Cre;Pten-loxP/loxP mice<br>2.Comparison of the gene expression profile in the proximal and distal part of normal prostates

2009-08-07 | E-MEXP-2029 | biostudies-arrayexpress

Chromatin immunoprecipitation using promoter microarrays to identify genes occupied by the transcriptional regulators HNF1a, HNF4a and HNF6, together with RNA polymerase II, in human liver and pancreatic islets

Project description:Here, we use chromatin immunoprecipitation combined with promoter microarrays to identify the genes occupied by the transcriptional regulators HNF1a, HNF4a and HNF6, together with RNA polymerase II, in human liver and pancreatic islets.

2004-07-15 | E-MEXP-68 | biostudies-arrayexpress

Chromatin immunoprecipitation of human cells after lipopolysaccharide stimulation, to identify binding of NF-KappaB family members

Project description:The NF-KappaB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-kappaB subunits act coordinately to regulate gene expression is based on a limited set of genes. We used genome-scale location analysis to identify targets of all five NF-kappaB proteins before and after stimulation of monocytic cells with bacterial lipopolysaccharide (LPS). In unstimulated cells, p50 and p52 bound to a significant number of gene promoters. p50 occupied genes together with RNA polymerase II and defined a set of genes to which other NF-kappaB proteins bound after LPS induction. In stimulated cells, genes bound by multiple NF-kappaB subunits exhibited the greatest increases in RNA polymerase II occupancy and gene expression. This study identifies novel NF-kappaB target genes, reveals how the different NF-kappaB proteins coordinate their activity and maps transcriptional regulatory networks that underlie the host response to infection.

2006-05-09 | E-WMIT-6 | biostudies-arrayexpress

Chromatin immunoprecipitation of human cell lines to identify cAMP-response element binding protein (CREB) binding sites.

Project description:Hormones and nutrients often induce genetic programs via signaling pathways that interface with gene-specific activators. Activation of the cAMP pathway, for example, stimulates cellular gene expression by means of the PKA-mediated phosphorylation of cAMP-response element binding protein (CREB) at Ser-133. Here, we use genome-wide approaches to characterize target genes that are regulated by CREB in different cellular contexts. CREB was found to occupy approximately 4,000 promoter sites in vivo, depending on the presence and methylation state of consensus cAMP response elements near the promoter. The profiles for CREB occupancy were very similar in different human tissues, and exposure to a cAMP agonist stimulated CREB phosphorylation over a majority of these sites. Only a small proportion of CREB target genes was induced by cAMP in any cell type, however, due in part to the preferential recruitment of the coactivator CREB-binding protein to those promoters. These results indicate that CREB phosphorylation alone is not a reliable predictor of target gene activation and that additional CREB regulatory partners are required for recruitment of the transcriptional apparatus to the promoter.

2006-05-09 | E-WMIT-11 | biostudies-arrayexpress

Chromatin immunoprecipitation of human HNF3b and E2F4, and mouse NeuroD1, for THEME analysis

Project description:Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover sequence patterns in the bound regions that may be recognized by the immunoprecipitated protein. However, the discovered motifs often do not agree with the binding specificity of the protein, when it is known. RESULTS: We present a powerful approach to analyzing ChIP-chip data, called THEME, that tests hypotheses concerning the sequence specificity of a protein. Hypotheses are refined using constrained local optimization. Cross-validation provides a principled standard for selecting the optimal weighting of the hypothesis and the ChIP-chip data and for choosing the best refined hypothesis. We demonstrate how to derive hypotheses for proteins from 36 domain families. Using THEME together with these hypotheses, we analyze ChIP-chip datasets for 14 human and mouse proteins. In all the cases the identified motifs are consistent with the published data with regard to the binding specificity of the proteins.

2006-05-09 | E-WMIT-8 | biostudies-arrayexpress

Chromatin immunoprecipitation of mouse and human cell lines and tissues using E2F4 antibodies

Project description:Despite being expressed in most tissues, a number of mammalian process-specific transcriptional regulators, such as those involved in cell cycle and immune responses, often have profound tissue-specific phenotypes. The mechanism underlying this effect is poorly understood. We chose to investigate on a genome-wide basis how the cell cycle master regulator E2F4, a key regulator of proliferation and differentiation in G0 cells, controls gene expression in multiple mammalian tissues. We identified potential direct targets of E2F4 in primary mouse and human tissues using chromatin immunoprecipitation. E2F4 binds a core set of genes in most mouse tissues that includes a substantial number of previously identified direct targets, and these common targets are highly enriched in the canonical binding sequence. Comparison of the genes bound in mouse tissues versus those bound in comparable human tissues revealed that, consistent with previous results, a core set of targets was bound in both species, and contains a substantial overrepresentation of cell-cycle genes.

2007-07-05 | E-TABM-272 | biostudies-arrayexpress

Chromatin immunoprecipitation of human MLL1 to understand its role in cell type specification

Project description:An experiment was performed to understand its role in cell type specification, we have determined the human genomic binding sites of MLL1. MLL1 localizes with Pol II to the 5' end of actively transcribed genes, where histone H3 lysine 4 (H3-K4) trimethylation occurs. The ability of MLL1 to serve as a start site-specific global transcriptional regulator and to participate in larger chromatin domains at the Hox genes reveals the dual roles MLL1 plays in maintenance of cellular identity.

2005-06-03 | E-WMIT-4 | 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