Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of human chondrocytes from patients with osteosarcoma or osteomyelitis, cultured in either 1% or 20% oxygen for one or four days

ABSTRACT: Cartilage was taken from the femoral condyle and tibial plateau from eight patients, cut into small pieces and digested overnight with Collagenase Type 2. The resultant chondrocytes were put through a cell strainer, pelleted and resuspended in fresh media and cultured for one week in 20% oxygen. The culture was split into five sub-cultures, one of which was immediately frozen; the remainder were allowed to recover overnight. Cells were subsequently grown at either 1% oxygen (hypoxia simulation) or 20% oxygen (normoxia simulation) for either one or four days before RNA extraction. Labelled RNA was then hybridised to Affymetrix Human U133 plus 2.0 arrays.

ORGANISM(S): Homo sapiens

DISEASE(S): osteosarcoma

SUBMITTER: Jayne Dennis

PROVIDER: E-MIMR-644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of human CD34+ stem/progenitor cell populations mobilized into the blood by granulocyte colony-stimulating factor

Project description:Mononuclear cells were isolated from granulocyte colony stimulating factor mobilised peripheral blood. CD34+ cells were selected and separated into adherent and non-adherent cells. Adherent and non-adherent samples were amplified and labelled using two IVT cycles, and gene expression profiling was performed by hybridisation to Affymetrix Human Genome U133 Plus2.0 Arrays.

2008-08-01 | E-MIMR-861 | biostudies-arrayexpress

Transcription profiling of human CD4CD45RO T-cells stimulated with interleukin-2, interleukin-6 or TNF-alpha and harvested at 24, 72 or 144 hours or stimulated with anti-CD3 antibodies and harvested at 24 hours

Project description:Blood taken from a healthy human donor was used to isolate CD4CD45RO T-cells. Purified cells were stimulated with either interleukin-2 (IL-2), Interleukin-6 (IL-6) and TNF-alpha and harvested at 24 hours, 72 hours (3 days) and 144 hours (6 days) or anti-CD3 antibodies and harvested at 24 hours. These were compared to unstimulated purified CD4CD45RO T-cells harvested at 0 hours.

2008-06-01 | E-MIMR-341 | biostudies-arrayexpress

Transcription profiling of mouse naive CD8+ T-cell differentiation during a primary immune response

Project description:Title: Gene Expression analysis of naive CD8+ T-cell differentiation during a primary immune response Description: C57BL/6 wild type mice are administered GK1.5 (depleting anti CD4 antibody) or isotope control by intraperitoneal injection at 3 and 1 day pre-infection, then every 36-48 hour post infection. 24 hours pre-infection, splenocytes from F5 RAG -/- mice are stained with CFSE and 10^7 splenocytes are transfered to recipient C57BL/6 mice by intravenous injection. 24 hours laters, recipient mice are infected with 10^7 PFU of a recombinant Vaccinia virus expressing NP366-74. At timepoints 0, 12, 24, 48, 72 and 96 splenocytes are obtained and FACS sorted to obtain CD8+ T-cells.

2005-09-29 | E-MIMR-38 | biostudies-arrayexpress

Transcription profiling of rat intestinal epithelial IEC-6 cells treated with non-steroidal anti-inflammatory agents to investigate gastrointestinal toxicity of NSAIDs

Project description:Non-steroidal anti-inflammatory drugs (NSAIDs) are used extensively as therapeutic agents, despite their well-documented gastrointestinal (GI) toxicity. Presently, the mechanisms responsible for NSAID-associated GI damage are incompletely understood. In this study, we used Microarray analysis to generate a novel hypothesis about cellular mechanisms that underlie the GI toxicity of NSAIDs. Monolayers of intestinal epithelial; cells (IEC-6) were treated with NSAIDs that either exhibit indomethacin, NS-398) or lack (SC-560) inhibitory effects on intestinal epithelial cell migration. Bioinformatic analysis of array data suggested that NSAIDs with adverse GI effects either decrease the gene expression of the calpains or increase the gene expression of the calpain engodenous; inhibitor, calpastatin. Calpains have been shown previously to modulate the migration of a variety of cells in different physiological contexts. Our experimental results suggest that the altered expression of calpain genes may contribute to the adverse effects of NSAIDs on intestinal; epithelial restitution. Microarray analysis has generated the novel hypothesis that the GI toxicity of NSAIDs may be attributed in part to drug-induced changes in the expression and activity of calpains. Experiment Overall Design: Monolayers of intestinal epithelial cells (IEC-6) were treated with NSAIDs that either exhibit (indomethacin, NS-398) or lack (SC-560) inhibitory effects on intestinal epithelial cell migration. Samples were then pooled to obtain sufficient material for gene array analysis. The pooled samples were used to hybridize 4 gene array chips for each biological sample.

2009-03-27 | E-GEOD-7584 | biostudies-arrayexpress

Identification of down stream genes in heat treated HSF triple mutants (hsfA1a, hsfA1b, and hsfA1d)

Project description:To characterize plant heat shock-responsive genes and to identify identified genes that are regulated by of HSFs underheat shock conditions, transcriptome analysis of rice was conducted using microarray. Arabidopsis plants were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.07â1.08) under a 16 h light/8 h dark photoperiod (50 Â± 10 Î¼mol photons mâ2 sâ1) at 22Â°C, and were treated for 30 min at 37Â°C.

2017-02-23 | E-MTAB-4505 | biostudies-arrayexpress

Transcription profiling of mouse pre-implantation development over twelve time points from the germinal vesicle (GV) stage oocyte to the late (expanded) blastocyst

Project description:The goal of the experiments was to profile and analyze gene activity during murine pre-implantation development. Samples were collected at twelve time points from the germinal vesicle (GV) stage oocyte to the late (expanded) blastocyst.

2004-02-19 | E-MEXP-51 | biostudies-arrayexpress

OsTZF1, a CCCH-Tandem Zinc Finger Protein gene, driven under own promoter produces no pleiotropic effects and confers salt tolerance in rice

Project description:The microarray was done using rice seedling plants grown in soil and treated with 250mM NaCl for two days.

2023-06-07 | E-MTAB-11842 | biostudies-arrayexpress

Gm heat 30 min & 5 h

Project description:control plants vs heat treated plants (30 min & 5 h)

2015-08-12 | E-MTAB-2852 | biostudies-arrayexpress

Identification of HS-responsive genes in rice

Project description:To characterize plant heat stress-responsive genes and to clarify the heat stress-responsive transcription pathways, the transcriptome analysis of rice was conducted using microarray. Rice (Oryza sativa L. cv. Nipponbare) were grown in plastic pots filled with nutrient soil for 2 weeks with a 12 h light (28Â°C)/12 h dark (25Â°C) regimen (ca. 1500 Î¼mol photons mâ2 sâ1) and were treated for 30 min at 42Â°C.

2017-02-23 | E-MTAB-4503 | biostudies-arrayexpress

Identification of down stream genes in heat treated NCED3 mutants

Project description:To characterize plant HS-responsive genes, the transcriptome analysis of rice was conducted using microarray. Arabidopsis plants were grown in plastic pots filled with peat moss for 3 weeks (principal growth stage 1.07â1.08) under a 16 h light/8 h dark photoperiod (50 Â± 10 Î¼mol photons mâ2 sâ1) at 22Â°C, and were treated for 30 min at 37Â°C.

2017-02-23 | E-MTAB-4506 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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