Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E14-adult rat hindlimb bud and transversus abdominis muscle

ABSTRACT: LCMS analysis of rat hindlimb buds (e14, e16) and transversus abdominis muscle (e18, e20, adult). Small (mg) pieces of tissue were solubilized with RapiGest (Waters), reduced, alkylated, and digested with trypsin. The resultant peptides were separated by HPLC and analyzed in data dependent MS mode using a Q Exactive mass spectrometer. The .raw LCMS files have been deposited.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rattus (ncbitaxon:10114)

SUBMITTER: Michael Previs

PROVIDER: MSV000095477 | MassIVE | Mon Jul 29 12:13:00 BST 2024

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Human and rat skeletal muscle multi-omic profiling

Project description:Skeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases and mobility. It is composed of several different cell and muscle fiber types. Here, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We additionally perform multi-omics profiling (gene expression and chromatin accessibility) on human and rat muscle samples.

| EGAS00001005730 | EGA

Drosophila indirect flight muscle

Project description:LC-MS/MS analysis of peptide digests of myofibrils from wild type and Dmlc2(Delta 2-46; S66A, S67A) mutant Drosophila flies. Myofibrils and thick filament samples were solubilized in 150 ul 0.1% RapiGest SF Surfactant (Waters Corporation; 50 C, 1 hour). Proteins were reduced by addition of 0.75 ul of 1M dithiothreitol and heating (100 C, 10 min). Cysteines were alkylated by addition of 22.5 ul of 100 mM iodoacetamide in 50 mM ammonium bicarbonate and incubation in the dark (22C, 30 min). Proteins were digested to peptides by addition of 25 ul of 50 mM ammonium bicarbonate containing 5 ug of trypsin (Promega) and incubating (37 C, 18 hours). The samples were dried down in speed vacuum device. Trypsin was deactivated and RapiGest was cleaved by addition of 100 ul of 7% formic acid in 50 mM ammonium bicarbonate and heating (37 C, 1 hour). The resultant peptides were dried down. RapiGest was cleaved again by addition of 100 ul of 0.1% trifluoroacetic acid and heating (37 C, 1 hour). The resultant peptides were dried down and reconstituted a final time in 60 ul of 0.1% trifluoroacetic acid. The samples were centrifuged at 18,800 RCF for 5 minutes (Thermo, Sorvall Legend Micro 21R) to pellet the surfactant. The top 57 ul of solution was transferred into a mass spectrometry (MS) analysis vial. A 20 ul aliquot of each sample was injected onto an Acquity UPLC HSS T3 column (100 A, 1.8 um, 1 x 150 mm) (Waters Corporation) attached to a UltiMate 3000 ultra-high pressure liquid chromatography (UHPLC) system (Dionex). The peptides were separated and the UHPLC effluent was directly infused into a Q Exactive Hybrid Quadrupole-Orbitrap mass spectrometer (MS) through an electrospray ionization source (Thermo Fisher Scientific). Data were collected in data-dependent MS/MS mode with the top five most abundant ions being selected for fragmentation.

2020-06-24 | MSV000085627 | MassIVE

Rat muscle atrophy

Project description:Transcriptional profiling of castrated rat cells (C3d) treated or not with testosterone for 8h (C3dpt8h) or 24h (C3dpt24h).

2020-04-09 | GSE97740 | GEO

In vitro differentiation of rat multipotent adult porgenitor cells to smooth muscle like cells

Project description:The aim of the study was to characterize the molecular mechanism involved in TGF-ß mediated smooth muscle formation in vitro. We employed rat bone marrow derived Oct4 expressing clones of multipotent adult progenitor cells (rMAPC). We subjected these cells to differentiation towards smooth muscle cell as previously reported using TGF-ß1. The differentiation process reuires 6 days with media change every 2 days followed by RNA harvest. RNA was isolated using commercially available kits (Qiagen RNA easy micro kit). RNA integrity and quality was assessed prior to labeling and hybridization. As a control RNA from rat aortic smooth muscle cells was commercially obtained.

2012-10-09 | GSE32990 | GEO

Gene expression profile in the rat heart across hear regions [array]

Project description:To characterize a expression patterns in the heart, we used rat. 12 Wistar male rats (8 - 11 weeks) were sacrificed. Left atrium (LA) adjacent to the pulmonary vein (PV), a mass of left ventricle (LV), and free-wall of the right ventricle (RV) was isolated. Each LV mass was dissected into three pieces as samples. Because the SAN isolation procedure takes approximately 20 minutes, SA was isolated separately. The SA region was delimited by the borders of the crista terminalis, the interatrial septum, the superior vena cava, and right atrium (RA). In addition to PV, LV, RV, SA, and RA samples, pulmonary arteries were added to the samples for the rat microarray.

2022-06-22 | GSE203369 | GEO

Transcription profiling of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall)

Project description:Comparison of normal adult rat extraocular muscle, cardiac muscle, leg (gastrocnemius-soleus) muscle and smooth muscle (stomach wall). Affymetrix microarray chip RG-U34A was used. MAS version 5 was used to analyze the muscle group differences. Data form part of publication: FASEB Journal 17: 1370-1372, 2003 (full length article available at http://www.fasebj.org/cgi/doi/10.1096/fj.02-1108fje).

2007-10-27 | E-GEOD-142 | biostudies-arrayexpress

Rat muscle proteome with salbutamol

Project description:We have performed a study on the effects of salbutamol (an anabolic agent) on the proteome of rat muscle cells. Salbutamol is a type of beta2 adrenergic agonist, which is known to cause hypertrophy in muscle. This is the 24h post treatment timepoint.

2011-03-18 | PRD000360 | Pride

Gene expression analysis of hyper active mutant SPORTS rat [muscle]

Project description:To get insight into the genetic characteristics of hyper active mutant line of rat, SPORTS, and the effect of exercise on gene expression, we compared gene expression profiles of exercised SPORTS rat, sedentary SPORTS rat, and sedentary wild type rat. Using RNA extracted from the muscle of these rats, we performed microarray analysis. Subsequent GO analyses revealed that genes belonging to muscle development and glycolysis were upregulated in exercised SPORTS rat compared to sedentary SPORTS rat, and genes related to coagulation were upreguated in sedentary SPORTS rat compared to wild type rat. These results were consistent with phenotypes, such as hyper activity and thrombotic tendency, which were reported for SPORTS rat.

2018-11-01 | GSE88853 | GEO

Rat lung cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

Project description:Rat somatic lung cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic lung cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic lung cells and rat iPS cells.

2009-04-01 | GSE13573 | GEO

Rat heart cells' gene expression difference compared with that of the adult cells including rat BMC and PEF cells

Project description:Rat somatic heart cell had different gene expression level compared with that of the adult cells including rat bone marrow cells(BMC) and rat primary ear fibroblasts(PEF). This difference gave the rat somatic heart cell unique characteristics which could then be compared with the rat iPS cells by genes comparison to show the gene expression difference between rat somatic heart cells and rat iPS cells.

2009-04-01 | GSE13572 | 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