Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dystrophin domains R4-15 and R20-23

ABSTRACT: Goal was to assess protein linkers between microtubules and dystrophin (specifically dystrophin regions R4-15 and R20-23). Two paired 10-plex TMT experiments were used to compare sixteen unique Dystrophin Glycoprotein Complex (or microtubule) enrichments (four genotypes, each with n=4) plus four pooled samples to allow comparison across the two individual 10-plex experiments for microtubules or DGC. A pair of 10-plex TMT(20 tags total) for the DGC enrichements, and a second pair of TMT (20 tags) for the MT enrichments. Samples are gastroc skeletal muscle from mouse.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: D'anna Nelson

LAB HEAD: Dr. James Ervasti

PROVIDER: PXD021088 | Pride | 2020-09-21

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	checksum.txt	Txt
	jervasti_dmnelson_16925_16926_WGA1and2.sf3	Other
	jervasti_dmnelson_16925_TMT_10-26_rerun.raw	Raw
	jervasti_dmnelson_16925_TMT_11-27_rerun.raw	Raw
	jervasti_dmnelson_16925_TMT_12-28.raw	Raw

Items per page:

1 - 5 of 67

Similar Datasets

EThcD-sceHCD-MS/MS-based Clinical N-glycoproteomics

Project description:Site-specific N-glycosylation characterization requires intact N-glycopeptide analysis based on suitable tandem mass spectrometry (MS/MS) method. Electron-transfer/higher-energy collisional dissociation (EThcD), stepped collision energy/higher-energy collisional dissociation (sceHCD), and higher-energy collision dissociation-product-dependent electron-transfer dissociation (HCD-pd-ETD) have emerged as valuable approaches for clinical glycoproteomics. However, each of them incurs some compromise, necessitating the performance comparisons when applied to the analysis of complex clinical samples (e.g., plasma, urine, cells, and tissue). Herein, we developed a hybrid mass spectrometry fragmentation method, EThcD-sceHCD, by combining EThcD and sceHCD. Moreover, we compared the performance of this method with those previous approaches (EThcD, sceHCD, HCD-pd-ETD, and sceHCD-pd-ETD) in the intact N-glycopeptide analysis, and determined its applicability for clinical N-glycoproteomic study.

2022-04-04 | PXD030288 | Pride

Effect of depletion of clpP2, clpX and clpC1 genes on whole cell proteome profile of Mycobacterium tuberculosis H37Rv

Project description:Global protein alteration in Mycobacterium tuberculosis H37 RV ( Mtb-H37RV) having depletion of Clpx ,Clp2 and ClpC1 were accessed using 4 plex iTRAQ label.

2020-05-14 | PXD013589 | Pride

The Trypanosoma cruzi Antigen and Epitope Atlas: fine characterization of antibody specificities in human Chagas Disease patients across human populations

Project description:These assays represent antibody-binding assays to analyze seroprevalence of antigens and epitopes at the individual level and also to perform fine epitope mapping characterizations. In this screening 392,299 peptides derived from reactive (antigenic) regions of Trypanosoma cruzi proteins were displayed in the form of short peptides (tiling array, overlapped) and assayed with individual serum samples (antibodies) from Chagas Disease patients across the Americas. Sectorized peptide arrays (QX12-plex slides, Roche Nimblegen) were incubated with serum samples (primary antibodies), washed, and then incubated with a fluorescently-labeled anti-human IgG commercial antibody (secondary antibodies). Raw readouts of fluoresence (signal), as well as normalized signal values are provided in this submission for all samples analyzed. All samples were analyzed in duplicate (r1 = replicate 1; r2 = replicate 2).

2022-08-20 | E-MTAB-11655 | biostudies-arrayexpress

Global proteomic profile of antibiotic induced persistent Mycobacterial sapmles

Project description:Global protein alteration in Mycobacterium tuberculosis H37 RV ( Mtb-H37RV) of day 2 (control) and day 16 (persistent) samples (in duplicates) treated with antibiotics 8µg/ml of ciprofloxacin and 0.1 µg/ml of Isoniazid (to mimic persister stage) were accessed using 4 plex iTRAQ label.

2021-07-29 | PXD013621 | Pride

HIF-2alpha Knockdown in A498 (VHL-/-) ccRCC cells

Project description:HIF-2alpha is essential for (VHL-/-) ccRCC subcutaneous tumor growth in mice, and in tumor cell lines, its inhibition results in increased ROS accumulation, tumor cell death and responsiveness to radiation treatment. We have utilized transcriptional profiling to screen for putative HIF-2alpha targets genes that serve an anti-oxidant and, thus, cell survival function. A498 ccRCC cell line was treated with control siRNA or mixture of two HIF-2alpha specific siRNA for 48 hours, and RNA was harvested. 4 independent experiments were performed, and expression was compared between control and HIF-2alpha knockdown groups. 8 total samples were applied to Affymetrix Human Gene 1.0 ST Arrays. We performed two-class paired analysis using Significance Analysis of Microarrays (SAM) software to compare expression in the CT (control siRNA) and H2 (Hif2-alpha siRNA) groups.

2009-08-27 | E-GEOD-16622 | biostudies-arrayexpress

Global proteomic analysis for stress response of Mycobacterium tuberculosis

Project description:To expand an insight into the stress adaptation in Mycobacterium tuberculosis H37Rv (Mtb), we approached the iTRAQ analysis to understand the global proteome profile of stressed Mtb under Acid (5.5 pH), Diamide (5mM) and Hydrogen peroxide (H2O2) (5mM) conditions and compared with gene expression of Mtb incubated in 7H9 rich medium (pH 7.0). The experiment was performed for overnight treatment of aforementioned stress. Whole cell lysate (WCL) from three independent repeats of control and stressed samples were labelled with three set of 4-plex iTRAQ labelling reagents (AB SCIEX) in proportion to manufacturer’s protocol.

2022-10-13 | PXD015167 | Pride

RT quantitative PCR analysis of Rosveratrol plus N-acetylcysteine of oxidative stress and inflammation genes in rat choclea.

Project description:Two month-old male Wistar rats received either resveratrol (10 mg/kg) plus N-acetylcysteine (400 mg/kg) or vehicle during 5 consecutive days. The second day of treatment, a concentrated solution of kanamycin and furosemide was placed on the round window of the right ears of rats receiving treatment or vehicle. Hearing was assessed by recording auditory brainstem responses before and 5, 16 and 23 days after starting the treatment with resveratrol and N-acetylcysteine. Cochlear samples were taken at the end of the treatment (5 days) and once the treatment had been suspended (23 days) to study cochlear cytoarchitecture and the evolution of the expression of oxidative stress, antioxidant defense and inflammation genes by using PCR arrays and RT-qPCR. qPCR gene expression profiling. Cochlea samples from 3-6 animals per group were analised. The expression of genes related to oxidative stress, antioxidant defense, and inflammation was studied at 5 and 23 days after the initiation of the 5 days treatment with resveratrol plus NAC.

2016-07-29 | E-GEOD-84925 | biostudies-arrayexpress

Concentrations of 27 cytokines and chemokines in the culture medium of HUVECs

Project description:Culture medium of HUVECs was collected and analyzed with the Bio-Plex Pro™ Human Cytokine 27-plex Panel.

2023-11-07 | GSE246852 | GEO

Dystrophin isoform Dp71eΔ71 is involved in the neurite outgrowth and neuronal differentiation of PC12 cells

Project description:The Dp71 protein is the most abundant dystrophin in the central nervous system (CNS). Several dystrophin Dp71 isoforms have been described and are classified into three groups, each with a different C- terminal end. However, the functions of Dp71 isoforms remain unknown. In the present study, we analyse the effect of Dp71eΔ71 overexpression on the neuronal differentiation of PC12 Tet-On cells. Overexpression of the dystrophin Dp71eΔ71 stimulates neuronal differentiation, increasing the percentage of cells with neurites and the neurite length. According to the 2-DE analysis, Dp71eΔ71 overexpression modified the protein expression profile of PC12 Tet-On cells that had been treated with neuronal growth factor (NGF) for nine days. Interestingly, all differentially expressed proteins were up-regulated compared to the control. The proteomic analysis showed that Dp71eΔ71 increases the expression of proteins with important roles in the differentiation process, such as the HspB1, S100A6, and K8 proteins involved in the cytoskeletal structure and the HCNP protein involved in neurotransmitter synthesis. The expression of the neuronal marker TH was also up- regulated.

2018-04-09 | PXD009114 | Pride

Proteome profiling of 2 dystrophic mouse models

Project description:Proteome profiling of tibialis anterior muscle from C57BL/6 mice and two dystrophin strains (mdx52 and mdx) at 8, 16, and 80 weeks in triplicates. TMT10 plex quantification and IPG-IEF pH 3.7-4.9 fractionation of peptides before nanoLC-MS/MS analysis on an Q-exactive instrument.

2020-10-01 | PXD017169 | JPOST Repository

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