Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome profiling of 2 dystrophic mouse models

ABSTRACT: 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.

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Thomas Roberts

PROVIDER: PXD017169 | JPOST Repository | Thu Oct 01 00:00:00 BST 2020

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	HJTRMW_TMT10-Wt-mdx-mdx52_set1_6w_250ug_IEF_37-49_50min_fr17.raw	Raw
	HJTRMW_TMT10-Wt-mdx-mdx52_set1_6w_250ug_IEF_37-49_50min_fr18.raw	Raw
	HJTRMW_TMT10-Wt-mdx-mdx52_set1_6w_250ug_IEF_37-49_50min_fr19.raw	Raw
	HJTRMW_TMT10-Wt-mdx-mdx52_set1_6w_250ug_IEF_37-49_50min_fr20.raw	Raw
	HJTRMW_TMT10-Wt-mdx-mdx52_set1_6w_250ug_IEF_37-49_50min_fr21.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Proteomics of late signaling responses decipher the roles of Cbl and Cbl-b in neuroblastoma cell differentiation

Project description:We applied quantitative mass spectrometry (MS)-based proteomics to study the roles of Cbl and Cbl-b in long-term signaling responses related to neurite outgrowth and differentiation of SH-SY5Y neuroblastoma cells. Using stable isotope labeling by amino acids in cell culture (SILAC) and tandem mass tag (TMT)-labeling in combination with off-line high-pH reversed-phase fractionation and LC-MS/MS we analyzed how Cbl and Cbl-b depletion by siRNA affected the proteome, phosphoproteome and ubiquitylome of the neuroblastoma cells. SILAC proteome SILAC (Light Arg0/Lys0, medium Arg6/Lys4, heavy Arg10/Lys8) SH-SY5Y cells were treated with Cbl and Cbl-b or control (GFP) siRNA for 72 hours. For combined stimulation with ligand cocktail (FGF-2, IGF-1 PDGF-BB, TGFα) cells were treated with ligands for 48 h. Samples were analyzed in triplicates with set-up as described below: Set-up 1, 3 replicates (R1-3): Light: siGFP, Heavy: siCbl/siCbl-b Set-up 2, 3 replicates (E1-3): Light: siGFP + ligand cocktail, Medium: siCbl/siCbl-b, Heavy: siCbl/siCbl-b + ligand cocktail TMT phosphoproteome and proteome SH-SY5Y cells were treated with Cbl and Cbl-b siRNA, control (GFP) siRNA or Retinoic acid (RA) for 24 hours. Samples were prepared in triplicates and labelled with TMT10-plex reagents according to the set-up below: TMT10-126: siGFP E1 TMT10-127N: siCbl/siCbl-b E1 TMT10-127C: Retinoic acid E1 TMT10-128N: siGFP E2 TMT10-128C: siCbl/siCbl-b E2 TMT10-129N: Retinoic acid E2 TMT10-129C: siGFP E3 TMT10-130N: siCbl/siCbl-b E3 TMT10-130C: Retinoic acid E3 TMT10-131: Mix of the 9 samples SILAC Ubiquitin pulldown SILAC (Light Arg0/Lys0, heavy Arg10/Lys8) SH-SY5Y cells were treated with Cbl and Cbl-b or control (GFP) siRNA for 24 hours. Samples were analyzed in duplicates with set-up as described below: Light: siGFP, Heavy: siCbl/siCbl-b

2021-03-30 | PXD020389 | Pride

Proteome characterization of Breast Cancer Cell lines

Project description:Protein profiling of 18 breast cancer cell lines in triplicates using TMT10-plex.

2020-07-04 | PXD013276 | JPOST Repository

Proteomic profiling of glioblastoma stem cells, human astrocyte, and T98G glioblastoma cell line

Project description:With HiRIEF LC-MS/MS shotgun proteomics, we analysed 6 patient-derived glioblastoma stem cells (BT stem cells) and compared them to an astrocyte line (CliniSciences, Guidonia Montecelio, Italy) and a more differentiated glioblastoma cell line (T98G). Each of the 8 cell line sample was run in triplicates in a total of three TMT10 sets, assigning each replicate in a separate TMT10 set, using 2 internal standards per set. The three TMT10 sets were ran in two experiments, first on immobilized pH gradient (IPG) 3-10 isoelectric focusing (IEF) strips, and then on IPG 3.7-4.9 IEF strips.

2022-12-23 | PXD027335 | Pride

The effect of RPN9 silencing in N. benthamiana

Project description:N. benthamiana plants were grown under 16 hour light/8 hour dark cycle in a plant growth room at 24°C for approximately six weeks before subjected to virus-induced gene silencing. Agrobacterium stain GV2260 (OD600=1.0) carrying silencing constructs were infiltrated into 2 fully expended leaves for inducing gene silencing. Samples were collected at 8, 10, 12, 14, and 16 days post Agro-inoculation (DPI) for RPN9-silenced plants and N-silenced control. For RPN8-silencing, samples were collected at 8, 10, and 12 DPI, and the empty vector treated plants were used as a control. Each sample was a pool of 6 silenced leaves collected from 3 individual plants. All the samples were in biological triplicates from 3 sets of independently silenced plants. Total RNA was extracted using Trizol and DNA was removed with DNase I treatment before cDNA synthesis. Keywords: Reference design

2007-09-01 | GSE8259 | GEO

Pregnancy changes expression in peripheral blood mononuclear cells of Multiple Sclerosis (MS) patients

Project description:Background: pregnancy is associated with reduced activity of multiple sclerosis (MS). However, the biological mechanisms underlying this pregnancy-related decrease in disease activity are poorly understood. This data series contains the subset of data used to generate a MS signature comparing female MS specimens before pregnancy with respect to female MS specimens at ninth month pregnancy. Subjects were followed in the outpatients clinic and blood was collected before pregnancy and at the following time points during pregnancy: first trimester (gestational age at sampling 12 weeks), second trimester (24 weeks), and third trimester (36 weeks). Before-pregnancy samples were obtained in a treatment-free period and after anticonceptional drug withdrawal. Peripheral blood mononuclear cells (PBMCs) obtained from 17 women (8 MS patients before pregnancy and 9 MS patients at 9th month pregnancy) were analyzed by oligonucleotide microarray technology.

2010-01-10 | E-GEOD-17410 | biostudies-arrayexpress

Rat models of cardiac hypertrophy

Project description:Cardiac hypertrophy was induced by aortic banding (6, 12, 16, and 30 weeks), myocardial infarction (3 and 9 weeks), an av-fistula (aorta abd. to v. cava inf.. 3 and 8 weeks), or hormone infusion (two weeks either angiotensin 2 or a thyroxin analogue). Sham operated or saline infused animals served as controls. Gene expression was determined by Affymetrix RGU34A GeneChip's to identify genes with common regulation in the different models of cardiac hypertrophy. Keywords: other

2004-03-12 | GSE738 | GEO

Transcription signature of Multiple Sclerosis in peripheral blood mononuclear cells.

Project description:Background: pregnancy is associated with reduced activity of multiple sclerosis (MS). However, the biological mechanisms underlying this pregnancy-related decrease in disease activity are poorly understood. This data series contains the subset of data used to generate a MS signature comparing female healthy specimens with respect to MS patients Subjects were followed in the outpatients clinic and blood was collected before pregnancy and at the following time points during pregnancy: first trimester (gestational age at sampling 12 weeks), second trimester (24 weeks), and third trimester (36 weeks). Before-pregnancy samples were obtained in a treatment-free period and after anticonceptional drug withdrawal. Peripheral blood mononuclear cells (PBMCs) obtained from 15 women (8 MS patients and 7 healthy controls) were analyzed by oligonucleotide microarray technology.

2010-01-10 | E-GEOD-17393 | biostudies-arrayexpress

Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity [miRNA data]

Project description:Analysis of skeletal muscle miRNA expression from type 2 diabetic volunteers before and after 16 weeks of chronic exercise training (two groups, one undergoing aerobic ecercise and the other resistance training exercise)

2014-09-10 | GSE58248 | GEO

Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity [Methylation data]

Project description:Analysis of skeletal muscle DNA methylation from type 2 diabetic volunteers before and after 16 weeks of chronic exercise training (two groups, one undergoing aerobic excercise and the other resistance training exercise)

2014-09-10 | GSE58280 | GEO

Multi-Omic Integrated networks connect DNA methylation and miRNA with skeletal muscle plasticity to chronic exercise in type 2 diabetic obesity [mRNA data]

Project description:Analysis of skeletal muscle gene expression from type 2 diabetic volunteers before and after 16 weeks of chronic exercise training (two groups, one undergoing aerobic ecercise and the other resistance training exercise)

2014-09-10 | GSE58249 | GEO

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