Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative global transcriptomic profiling of mild and severe neurotrauma in an in vitro neuronal model

ABSTRACT: Traumatic brain injury is one of the common cause of adult permanent disability. As its physio-pathological mechanism has yet to be elucidated, by adopting microarray technique we hope to decipher the novel signaling cascades involved, and if different severity of injury would induce any form of neuronal regeneration. Microarray was performed on 34 arrays on Illumina Rat Ref12V1 expression beadchips. 6 control samples were adopted as universal controls, and n=3 was used for each time-points (0h, 8h, 15h, 24h and 48h) for Mild neurotrauma and (8h, 15h, 24h and 48h) for Severe neurotrauma. Only one replicate is present for 0h Severe neurotrauma.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Minghui Jessica Chen

PROVIDER: E-GEOD-23653 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Comparative global transcriptomic profiling of low and high concentration of lactacystin-mediated neuronal death

Project description:Inhibition of proteasome degradation pathway has been implicated in neuronal cell death leading to neurodegenerative diseases such as Parkinson’s disease and Alzheimer’s disease. Pharmacological proteasomal inhibitors such as lactacystin can induce apoptosis in cultured mouse cortical neurons through the activation of caspase-3. However, Meiners et al., 2003 suggested that low dose of lactacystin induces a concerted expression of proteasome genes and de novo formation of proteasomes. We discovered by microarray analysis that lactacystin treatment induces a dose-dependent biphasic modulation of both potentially neuroprotective as well as pro-apoptotic genes in neurons. Microarray analysis was carried out using 24 Illumina mouse Ref8V1.1 genechip arrays. The assignment of the arrays was as follows: Controls (n=6); exposure to 1 ?M (High) lactacystin for 5h, 8h, 15h and 24 h (n=3 respectively) and 0.1uM (Low) for 15h and 24h (n=3 respectively).

2013-12-31 | E-GEOD-23155 | biostudies-arrayexpress

Global transcriptomic profiling of oxygen-glucose deprivation (OGD)-mediated neuronal injury

Project description:Oxygen-glucose deprivation (OGD) is a cellular phenomenon consistently observed upon occurrence of ischemic stroke which eventually results in neuronal death. Neuronal cell death after ischemia takes place via two distinct processes, necrosis and apoptosis. Apoptosis, programmed cell death, is denoted by chromatin condensation, nuclear blebbing, cellular shrinkage, and DNA fragmentation. Unlike apoptosis, cellular swelling and lysis is suggestive of necrosis. However, these two processes are related not only to the severity but also to the duration of ischemia. Microarray analysis was carried out using 20 Illumina mouse Ref8V1.1 genechip arrays. The assignment of the arrays was as follows: Controls (n=5); exposure to OGD for 10min, 5h, 8h, 15h and 24 h (n=3 respectively).

2013-12-31 | E-GEOD-23158 | biostudies-arrayexpress

Global gene profiling of glutamate-induced neuronal death

Project description:Glutamate, a major neurotransmitter in the mammalian nervous sytem, has been involved in the mediation of excitotoxicity commonly observed in the pathogenesis of stroke. Current study focused on gaining an insight into the molecular mechanisms of glutamate-induced neuronal death A total of 15 RNA samples were analyzed. There is one treatment conditions of 250uM glutamate. 3 replicates were collected for each of the selected time-points (5h, 15h and 24h) in addition to 6 replicates of shared vehicle control.

2013-12-31 | E-GEOD-19936 | biostudies-arrayexpress

Transcription profiling of cumulus cell oocyte complexes isolated at different time points of ovulation to identify differentially expressed genes.

Project description:Cumulus-oocyte complexes were isolated at seperate time-points to generate temporal complexes. Targets from two biological replicates at each time point (0h, 8h, 16h post-hCG treatment) were generated and the expression profiles were determined using Affymetrix GeneChip Mouse Genome 430 2.0 Arrays. Comparisons between the sample groups allow the identification of genes with temporal expression patterns. Experiment Overall Design: 2 eCG-primed (48h) pooled cumulus-oocyte complexes, 2 eCG-primed (48h) hCG-treated (8h) pooled cumulus-oocyte complexes, and 2 eCG-primed (48h) hCG-treated (16h) pooled cumulus-oocyte complexes replicates were analyzed

2007-11-06 | E-GEOD-4260 | biostudies-arrayexpress

Erk-dependent transcriptome

Project description:Transcriptome analysis of ESCs harboring an 4OHT-inducible cRAF for 0h, 8h, 10h, or 8h followed by a 2h inhibition with a chemical inhibitor

2019-08-08 | GSE110662 | GEO

Global gene profiling comparison between hydrogen sulfide- and N-methyl-D-aspartate-induced neuronal deaths

Project description:Hydrogen sulfide (H2S), present in abundance in the mammalian brain, has recently been demonstrated to induce a dose- and time-dependent apoptotic-necrotic continuum in murine primary cortical neurons, which was successfully attenuated upon application of N-methyl-D-aspartate (NMDA) receptor antagonist. The current study focused on gaining an insight into the molecular mechanisms of H2S–mediated neuronal death pertaining to NMDA receptors activation through global gene expression comparisons. A total of 24 RNA samples were analyzed. There are 2 treatment conditions, namely 200uM sodium hydrosulfide and 200uM N-methyl-D-asparate. 3 replicates were collected for each of the selected time-points (5h, 15h and 24h), in addition to 6 replicates of shared vehicle control. The supplementary file 'GSE16035_non-normalized_data.txt' contains non-normalized data for Samples GSM401312-GSM401335.

2013-01-23 | E-GEOD-16035 | biostudies-arrayexpress

Spen regulates X chromosome inactivation (CUT&RUN)

Project description:CUT&RUN on Spen-degron TX1072 mESCs was performed in 2 biological replicates. Cells were treated with doxycycline (1ug/mL) for 0h, 4h, 8h, 24h and 8h doxycycline and auxin (500uM).

2019-12-08 | GSE131782 | GEO

Hepatocytes-HepaRG reprogramming.

Project description:To identify the molecular mechanisms and environmental inducers contributing to reprogramming of hepatocytes into progenitors in HCC context, we used the HepaRG cell line as model. We performed transcriptomic analysis at various time-points during this process; 0h, 1h, 4h, 8h, 12h, 16h, 24h and 48h.

2013-12-05 | E-GEOD-52989 | biostudies-arrayexpress

miRNA profiling of control and ischemic samples in vitro and in vivo

Project description:miRNA microarray profiling of primary cortical neurons exposed to 4h oxygen and glucose deprivation (OGD) in vitro. RNA samples collected at 8h post-OGD terminaion. miRNAs were also profiled in mice exposed to 3- vessel occlusion model of stroke. RNA samples collected from contralateral (control) and ipsilateral (infarct) sides of the brain following 24h of reperfusion. Comparison of control and ischemic samples across 3 biological replicates for both in vitro and in vivo samples. In vitro cultures consisted of primary cortical neurons derived from E17 rat Wistar embryos. In vivo samples were obtained from C57bl/6 mice exposed to three-vessel occlusion.

2013-11-21 | E-GEOD-51586 | biostudies-arrayexpress

Immediate adaption – Quantitative Proteomics of BCL6 silencing and EGFR TK inhibition

Project description:We aimed to identify the response mechanism to EGFR tyrosine kinase inhibition. A431 cells were transfected with mock siRNA or BCL6 siRNA. Cells were then treated with gefitinib. Harvesting was done at 0h, at 24h and at 48h. Two TMT10plex sets were organized as follows: TMT set1: mock 0h (3x, channels 126, 127N and 127C), mock 24h (3x, 128N, 128C and 129N), mock 48h (3x, 129C, 130N, 130C) and internal pooled standard (131) composed from equal aliquots of all samples (mock siRNA and BCL6 siRNA). TMT set2: siBCL6 0h (3x, channels 126, 127N and 127C), siBCL6 24h (3x, 128N, 128C and 129N), siBCL6 48h (3x, 129C, 130N, 130C) and the same internal pooled standard (131) as for set 1.

2020-12-09 | PXD016605 | Pride

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