Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of mouse myotubes grown under control and starvation conditions

ABSTRACT: C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2. Cells were plated at a density of 40-50% in 100mm dishes. When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4). Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed. After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and starved (non re-fed cells)

ORGANISM(S): Mus musculus

SUBMITTER: Susan Kandarian

PROVIDER: E-GEOD-1776 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptional profile of a myotube starvation model of atrophy.

Stevenson Eric J EJ Koncarevic Alan A Giresi Paul G PG Jackman Robert W RW Kandarian Susan C SC

Journal of applied physiology (Bethesda, Md. : 1985) 20041217 4

Skeletal muscle wasting is a pervasive phenomenon that can result from a wide range of pathological conditions as well as from habitual muscular inactivity. The present work describes a cell-culture condition that induces significant atrophy in skeletal muscle C2C12 myotubes. The failure to replenish differentiation media in mature myotubes leads to rapid atrophy (53% in diameter), which is referred to here as starvation. Affymetrix microarrays were used to develop a transcriptional profile of c ...[more]

PMID: 15608089

Similar Datasets

Control and starved myotubes

Project description:C2C12 mouse myoblasts (American Type Culture Collection, Manassas, VA) were maintained in growth medium (DMEM supplemented with 10% Fetal Bovine serum, Invitrogen Corporation, Carlsbad, CA) in 5% CO2. Cells were plated at a density of 40-50% in 100mm dishes. When cells reached ~90% confluency 24 hours later, they were switched to differentiation media (DMEM containing 2% horse serum; GIBCO, Invitrogen Corporation, Carlsbad, CA) which was subsequently changed every 48 hours. All cells were allowed to differentiate for 4 days with feeding every two days (day 0, 2, and 4). Beginning at day 4, control cells were re-fed every 48 hours whereas experimental cells were not re-fed. After an additional 4 days (8 days post differentiation), cells were harvested and total RNA was isolated from control and "starved" (non re-fed cells) Keywords: repeat sample

2004-09-20 | GSE1776 | GEO

Transcriptomic analysis of Wild type M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv

Project description:Gene expression microarray was performed using early log phase culture at 37 degree and 200 rpm followed by RNA extraction from M.tb H37Rv, HigB KO M.tb H37Rv and complemented Hig B KO M.tb H37Rv For gene expression profiling, total RNA was isolated from wild type H37Rv, higB KO mutant strain and complemented strains. The bacterial pellets for M.tb H37Rv wild type, M.tb H37Rv HigB KO mutant strain and complemented strain were resuspended in 1.0 ml TRIzol (Invitrogen Corporation, Carlsbad, CA); mRNA was extracted as per standard protocols and cleaned using RNAeasy columns (Qiagen GmbH, Hilden, Germany). Extracted mRNA (1 μg) was treated with DNase I using the Ambion DNA-free kit (Invitrogen Corporation, Carlsbad, CA) to remove genomic DNA contamination and quantified using Nanodrop 2000c spectrophotometer (Thermo Scientific, USA). The purity and integrity of RNA samples were assessed Agilent 2100 Bio analyzer (Agilent TechnologiesInc., USA). Further, 25ng of RNA was amplified and labeled using Low input Quick Amp WT Labeling kit (Agilent Technologies, USA). The labeled cRNA was purified using RNAeasy columns (Qiagen, USA) and total yields were quantified using Nanodrop 2000c spectrophotometer.

2021-11-30 | GSE179403 | GEO

BR effects on WT and yucca seedlings

Project description:Ten-day old light-grown Arabidopsis seedlings were immersed in 1 µM brassinolide in one-half-strength Murashige Minimal Organics Medium (Invitrogen, Carlsbad, CA) or media alone for 2.5 hours Keywords: repeat sample

2004-08-31 | GSE862 | GEO

Osteoclast response to low extracellular sodium

Project description:RAW 264.7 murine osteoclastic cells were cultured with recombinant cytokines (RANKL and M-CSF) in culture medium with normal sodium (NS; Na=140 mmol/l) and low sodium and reduced sodium (Na=120 mmol.l) while maintaining normal ostmolality with the addition of mannitol. After 24 hours, total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags. Total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags.

2022-08-09 | GSE128152 | GEO

Niemann-Pick type C fibroblast analysis

Project description:Primary skin fibroblasts from four Niemann-Pick type C patients homozygous for the I1061T mutation and four control individuals were cultured under identical conditions in DMEM containing 10% fetal bovine serum. Cells were harvested at 50-70% confluency. mRNA was isolated with the FastTrack 2.0 mRNA isolation kit according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). A reference RNA comprised of 10 cell lines was used as the control for each hybridized sample (Stratagene, La Jolla, CA). Both sample and reference RNAs were amplified using the MessageAmp II aRNA amplification kit (Ambion, Austin, TX). Set of arrays that are part of repeated experiments Keywords: Biological Replicate

2007-08-15 | GSE8770 | GEO

H295R human adrenocortical cells treated with Angiotensin II, Potassium or Forskolin

Project description:H295R human adrenocortical cells were cultured in H295R complete media containing DMEM:F12 (1:1) supplemented with 2% Ultroser G (Biosepra, Villeneuve-la-Garenne, France), ITS-Plus (Discovery Labware, Bedford, MA) and an antibiotic/antimycotic mixture (Invitrogen, Carlsbad, CA) in 175 cm2 flasks until subconfluente. Media was replaced with 40 ml fresh media containing different agents and cultured for 3 h. Treatments: Angiotensin II (100 nM), potassium (16 mM) and forskolin (10 uM). Total RNA extracted with RNAesy Midi Kit (Qiagen) with on-column DNase digestion Keywords: Agent response

2007-07-09 | GSE5553 | GEO

Predictors of the response to chemoradiotherapy in SCC of larynx

Project description:Laryngeal and hypopharyngeal squamous cell carcinoma was histopathologically confirmed on 35 samples obtained by incisional biopsy. Total RNAs from frozen specimens were isolated using Trizol reagent (Invitrogen Corporation, Carlsbad, CA) according to the manufacturer protocol. RNA quality was verified by electrophoresis through agarose gel upon visualization with ethidium bromide and only RNA samples with a ratio >1 for 28S/18S ribosomal RNA were further processed. A two-round RNA amplification procedure was carried out. Normal larynx and hypopharynx samples was used as reference for hybridizations, these samples were processed in the same manner as tumor samples. Amplified RNA were then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP Keywords: other

2005-05-09 | GSE2465 | GEO

AKT/PACS2 participates in renal vascular hyperpermeability by regulating endothelial fatty acid oxidation in diabetic mice

Project description:HUVECs were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA) and cultured in an Endothelial Cell Medium (Invitrogen, Carlsbad, CA, USA) containing 5% fetal bovine serum at 37°C in a 5% CO2 incubator. Cells were treated with 30 mM glucose and 0.1 mM palmitic acid (P0500, Sigma-Aldrich, USA) dissolved in 0.5% bovine serum albumin (BSA) for 48 h to simulate HGHF treatment. The Akt inhibitor MK-2206 2HCl was purchased from Selleck Chemicals (S1078, Houston, TX, USA).

2022-08-12 | PXD033227 | Pride

Effect of Exportin-5 expression on Mouse fibroblasts in cell cycle re-entry phase

Project description:To analyze the effect of Exportin-5 expression on the MEF cells in cell cycle re-entry phase, we have employed whole genome microarray expression profiling on the MEF cells in cell cycle re-entry phase with and without down regulation of Exportin-5 gene. Mouse MEF cells were transfected with 60nM of siRNA targeting either Exportin-5 or negative control, and incubated for 12 hours. After incubation, cells were starved with DMEM containing 0.2% FCS for 48 hours and re-fed with DMEM containing 20%FCS for 24 hours, along with second siRNA transfection. Two independant expreiments were preformed.

2013-01-01 | E-GEOD-25498 | biostudies-arrayexpress

Effects of plasticizers on adult human adipocytes (SGBS) using global proteomics

Project description:SGBS cells were used as a model system to investigate the cellular mode of action of a variety of plasticizers in human adipocytes. In brief, cells were cultured at 5% CO2 and 37°C in 95% humidity. Cells of generation 40 and passage 3 after thawing were grown to confluence with DMEM/F12 containing 33 µM biotin, 17 µM pantothenate, 100 U/l penicillin, and 0.1 mg/l streptomycin (basal medium) supplemented with 10% FCS (Gibco, Carlsbad, CA, USA). According to the standard differentiation protocol, differentiation was initiated (day 0) after changing to serum-free basal medium supplemented with 0.1 μM cortisol, 0.01 mg/ml apo-transferrin, 0.2 nM triiodothyronine, and 20 nM human insulin (differentiation medium) with the addition of 2 µM rosiglitazone, 25 nM dexamethasone, and 200 µM 3-isobutyl-1-methylxanthine for the first four days. SGBS cells were first differentiated according to the standard protocol for 12 days. Obtained adult adipocytes were then exposed to the plasticizers for 8 days with medium changes every second day. The control contained equivalent amounts of solvent (0.01% MeOH). Additinally, a control on day 12 before exposure was sampled. All SGBS cell culture experiments were conducted in quadruplets.

2022-06-20 | PXD030843 | Pride

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