Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phosphorylation of mouse TRPM7 in HEK293 overexpressed cell line

ABSTRACT: An investigation of phosphorylation patterns of the mouse ion channel TRPM7 using multiple extraction (SCAD and S-Trap) and enrichment techniques (titanium and iron columns).

INSTRUMENT(S): Thermo QExactive coupled with Agilent 1260 Infinity LC system

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Stephanie Cologna

PROVIDER: MSV000083384 | MassIVE | Thu Jan 31 12:21:00 GMT 2019

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

E-MTAB-7212

Project description:Investigation of titanium coated imprinted polystyrene surfaces

2019-02-11 | E-MTAB-7212 | ExpressionAtlas

Total RNA-sequencing Detects Transcriptome Differences in Mouse Preosteoblast Response to Bulk Nanostructured Titanium

Project description:Titanium is the most widely used alloy family in dental and orthopedic implants due to its natural ability to integrate into bone, but cytotoxic alloying elements are required in titanium for its mechanical properties to match the functionality of natural bone in high-load bearing applications. Recent advances in nanostructuring, such as Equal Channel Angular Pressing-Conform (ECAP-C), reduce the grain size and increase the strength of pure grades of titanium, thereby eliminating the need for cytotoxic elements and increasing cytocompatibilty as measured by traditional cell biology techniques. Transcriptomic profiling of cells grown on conventional coarse grain (CG) versus nanostructured ultrafine grain (UG) surfaces can simultaneously enhance our understanding of genomics and biomaterials, facilitating the development of a new generation of implantable materials. Sterile Ti discs, 13.5 mm in diameter and polished to a 2 nm average surface roughness were arrayed in a non-tissue culture treated 24-well cell culture plate using a block design, with 12 CG and 12 UG disks. Wells were re-fed after 24 hours and after 72 hours Ti discs were transferred to new plates for standard cell harvesting protocols. The cells from four wells were consolidated into one sample and were stored at -80°C in RNAlater. All subsequent steps were identical for all samples. Samples on CG were used as the control for UG-CG comparisons.

2020-01-02 | E-MTAB-7528 | biostudies-arrayexpress

Identification of Francisella tularensis genes affected by iron limitation

Project description:Three pairs of total RNA preparations from F. t. LVS grown under iron-replete and iron-restricted conditions were used in the DNA microarray. Seven arrays were used to examine the genes affected by iron limitation. Keywords: Dual Channel (Cy5/Cy3) arrays

2006-07-26 | GSE3622 | GEO

Evolution from adherent to suspension: systems biology of HEK293 cell line development.

Project description:The need for new safe and efficacious therapies has led to an increased focus on biologics produced in mammalian cells. The human cell line HEK293 has bio-synthetic potential for human-like production attributes and is currently used for manufacturing of several therapeutic proteins and viral vectors. Despite the increased popularity of this strain we still have limited knowledge on the genetic composition of its derivatives. Here we present a genomic, transcriptomic and metabolic gene analysis of six of the most widely used HEK293 cell lines. Changes in gene copy and expression between industrial progeny cell lines and the original HEK293 were associated with cellular component organization, cell motility and cell adhesion. Changes in gene expression between adherent and suspension derivatives highlighted switching in cholesterol biosynthesis and expression of five key genes (RARG, ID1, ZIC1, LOX and DHRS3), a pattern validated in 63 human adherent or suspension cell lines of other origin.

| S-EPMC7642379 | biostudies-literature

Phosphoproteome of filamentous fungus Aspergillus nidulans

Project description:We describe thephosphoproteome of filamentous fungus Aspergillus nidulans. Phosphopeptides were enriched using affinity enrichment using titanium dioxide and separated using a convenient ultralong gradient separations on c18 reverse phase columns. Over 1637 phosphopeptides corresponding to 647 phosphoproteins were identified using using a “high-high” strategy using HCD on the novel Q-exactive platform

2014-11-18 | PXD000715 | Pride

Space environmental factor impacts upon murine colon microbiota and mucosal homeostasis

Project description:We report how high and low linear energy transfer (LET) radiation, microgravity, and elevated dietary iron affect colon microbiota (determined by 16S rDNA pyrosequencing) and colon function. Three independent experiments were conducted: 1) fractionated low LET γ radiation (137Cs, 3 Gy, RAD), high Fe diet (IRON) (650 mg/kg diet), and a combination of low LET γ radiation and high Fe diet (IRON+RAD) in male Sprague-Dawley rats; 2) high LET 38Si particle exposure (0.050 Gy), 1/6 G partial weight bearing (PWB), and a combination of high LET38Si particle exposure and PWB in female BalbC/ByJ mice; and 3) 13 d spaceflight in female C57BL/6 mice. For each experiment, the colon was resected and feces removed for microbial sequencing analysis on a Roche 454 Genome Sequencer FLX Titanium instrument (Microbiome Core Facility, Chapel Hill NC) using the GS FLX Titanium XLR70 sequencing reagents and protocols. Analysis of amplicon sequencing data was carried out using the QIIME pipeline. Low LET radiation, high iron diet, and spaceflight increased Bacteroidetes and decreased Firmicutes. Low LET radiation, high Fe diet, and spaceflight did not significantly affect diversity or richness, or elevate pathogenic genera. Spaceflight increased Clostridiales and decreased Lactobacillales, and similar trends were observed in the experiment using a ground-based model of microgravity, suggesting altered gravity may affect colonic microbiota. Microbiota characteriztion in these models is a first step in understanding the impact of the space environment on intestinal health.

2015-11-30 | GSE68738 | GEO

Liver miRNA profiling in iron deficient and overload mice

Project description:8-week-old wild-type 129S6/SvEvTac mice were maintained under regular iron diet (containing 330 ppm iron) or iron-enriched diet (the same standard diet supplemented with 2% carbonyl iron) for 4 weeks. 7-week-old wild-type 129S6/SvEvTac mice were maintained under iron-deficient diet (with negligible iron content) for 5 weeks. All mice were sacrificed at the age of 12 weeks. Livers were harvested and total RNA was extracted using TRIZol method followed by miRNA-enrichment using Qiagen columns. Liver RNA samples from 3 mice (female and male) from each group were sent to Exiqon for microarray analysis.

2014-09-04 | E-MTAB-1520 | biostudies-arrayexpress

Transcription profiling of liver from wild type and Hfe-/- mice with hereditary hemochromatosis subjected to dietary iron overload and treatment with nifedipine to reverse iron overload

Project description:Hereditary hemochromatosis and transfusional iron overload are frequent clinical conditions associated with progressive iron accumulation in parenchymal tissues leading to eventual organ failure. We have discovered a novel mechanism to reverse iron overload by pharmacological modulation of the divalent metal transporter-1 (DMT-1). DMT-1 mediates intracellular iron transport during the transferrin cycle and apical iron absorption in the duodenum. Additional functions in iron handling in the kidney and liver are less well understood. We show that the L- type calcium-channel blocker nifedipine increases DMT-1 mediated cellular iron transport 10-to 100-fold at concentrations between 1-100 uM. Mechanistically, nifedipine causes this effect by prolongation of the activity of DMT-1 to transport iron. We show that nifedipine mobilizes iron from the liver of mice with primary and secondary iron overload, and enhances urinary iron excretion. Modulation of DMT-1 function by L-type calcium-channel blockers emerges a novel pharmacological concept to treat iron overload disorders.<br> <br> In this experiment mice were subjected to dietary iron overload before being treated with nifedipine at 5 ug/g bodyweight, or mock treated with the same volume of solvent.

2007-03-01 | E-MEXP-982 | biostudies-arrayexpress

Streptomyces coelicolor quantitative proteome and phosphoproteome analyses reveal proteins and phosphoproteins modulating differentiation and secondary metabolism

Project description:Investigation of proteome and phosphoproteome changes during Streptomyces coelictor life cycle using TMT tagging and calcium precipitation - titanium dioxide enrichment

2018-05-25 | PXD005558 | Pride

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis.

Project description:Structural studies of glycoproteins and their complexes provide critical insights into their roles in normal physiology and disease. Most glycoproteins contain N-linked glycosylation, a key post-translation modification that critically affects protein folding and stability and the binding kinetics underlying protein interactions. However, N-linked glycosylation is often an impediment to yielding homogeneous protein preparations for structure determination by X-ray crystallography or other methods. In particular, obtaining diffraction-quality crystals of such proteins and their complexes often requires modification of both the type of glycosylation patterns and their extent. Here, we demonstrate the benefits of producing target glycoproteins in the GlycoDelete human embryonic kidney 293 cell line that has been engineered to produce N-glycans as short glycan stumps comprising N-acetylglucosamine, galactose and sialic acid. Protein fragments of human Down syndrome cell-adhesion molecule and colony-stimulating factor 1 receptor were obtained from the GlycoDelete cell line for crystallization. The ensuing reduction in the extent and complexity of N-glycosylation in both protein molecules compared with alternative glycoengineering approaches enabled their productive deployment in structural studies by X-ray crystallography. Furthermore, a third successful implementation of the GlycoDelete technology focusing on murine IL-12B is shown to lead to N-glycosylation featuring an immature glycan in diffraction-quality crystals. It is proposed that the GlycoDelete cell line could serve as a valuable go-to option for the production of homogeneous glycoproteins and their complexes for structural studies by X-ray crystallography and cryo-electron microscopy.

| S-EPMC7709199 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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