Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

38 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of murine cerebellum to identify novel candidate genes for ethanol sensitivity QTLs.

ABSTRACT: Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol's actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to sleep time, the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol. Experiment Overall Design: Expression was assayed using the Affymetrix Expression Set 430 A and B arrays. Four mice were included in the experiment, two ILS and two ISS.

ORGANISM(S): Mus musculus

SUBMITTER: Erik James MacLaren

PROVIDER: E-GEOD-3071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs.

MacLaren Erik J EJ Bennett Beth B Johnson Thomas E TE Sikela James M JM

Mammalian genome : official journal of the International Mammalian Genome Society 20060207 2

The Inbred Long Sleep (ILS) and Inbred Short Sleep (ISS) mouse strains have a 16-fold difference in duration of loss of the righting response (LORR) following administration of a sedative dose of ethanol. Four quantitative trait loci (QTLs) have been mapped in these strains for this trait. Underlying each of these QTLs must be one or more genetic differences (polymorphisms in either gene coding or regulatory regions) influencing ethanol sensitivity. Because prior studies have tended to focus on ...[more]

PMID: 16465594

Similar Datasets

ILS/ISS Cerebellum Comparison Affy430

Project description:Inbred Long-Sleep (ILS) and Inbred Short-Sleep (ISS) mice exhibit a large difference in a number of alcohol and drug related behaviors. This study examined the expression levels of transcripts in these strains in the cerebellum, which is a major target of ethanol’s actions in the CNS, in order to find differentially expressed candidate genes for these phenotypes. Cerebellum was specifically chosen due to the fact that Purkinje cell sensitivity to ethanol in these strains is highly correlated to "sleep time", the measure of ethanol sensitivity used with these strains. Naive mice were used because differences in sensitivity are observed upon initial exposure to ethanol. Keywords: cerebellum, naive, untreated

2005-12-02 | GSE3071 | GEO

ILS/ISS cerebellum baseline comparison

2005-12-02 | GSE3114 | GEO

Mus musculus

Project description:ILS/ISS cerebellum baseline comparison

| PRJNA93123 | ENA

Mus musculus

Project description:ILS/ISS Cerebellum Comparison Affy430

| PRJNA93169 | ENA

Mus musculus breed:Inbred Long Sleep (ILS), Inbred Short Sleep (ISS)

Project description:Mus musculus breed:Inbred Long Sleep (ILS), Inbred Short Sleep (ISS) Raw sequence reads

| PRJNA353308 | ENA

Transcription profiling of mouse prefrontal cortex of C57Bl/6J mice at Zeitgeber Time (ZT) 3, 9, 15, and 21.

Project description:Background: The prefrontal cortex is important in regulating sleep and mood. Diurnally regulated genes in the prefrontal cortex may be controlled by the circadian system, by the sleep-wake states, or by cellular metabolism or environmental responses. Bioinformatics analysis of these genes will provide insights into a wide-range of pathways that are involved in the pathophysiology of sleep disorders and psychiatric disorders with sleep disturbances. Results: We examined gene expression in the mouse prefrontal cortex at four time points during the 24-hour (12-hour light:12-hour dark) cycle by microarrays, and identified 3,890 transcripts corresponding to 2,927 genes with diurnally regulated expression patterns. We show that 16% of the genes identified in our study are orthologs of identified clock, clock controlled or sleep/wakefulness induced genes in the mouse liver and SCN, rat cortex and cerebellum, or Drosophila head. The diurnal expression patterns were confirmed in 16 out of 18 genes in an independent set of RNA samples. The diurnal genes fall into eight temporal categories with distinct functional attributes, as assessed by the Gene Ontology classification and by the analysis of enriched transcription factor binding sites. Conclusions: Our analysis demonstrates that ~10% of transcripts have diurnally regulated expression patterns in the mouse prefrontal cortex. Functional annotation of these genes will be important for the selection of candidate genes for behavioural mutants in the mouse and for genetic studies of disorders associated with anomalies in the sleep:wake cycle and circadian rhythms. Experiment Overall Design: Prefrontal cortex from 3 biological replicates of C57BL/6J mice at four Zeitgeber Times (ZT 3, 9, 15, and 21) were analyzed

2008-06-16 | E-GEOD-9471 | biostudies-arrayexpress

Proteomic characterization of Aspergillus fumigatus isolated from air and surfaces of the International Space Station

Project description:The on-going Microbial Observatory Experiments on the International Space Station (ISS) revealed the presence of various microorganisms that may be affected by the distinct environment of the ISS. The low-nutrient environment combined with enhanced irradiation and microgravity may trigger changes in the molecular suit of microorganisms leading to increased virulence and resistance of microbes. Proteomic characterization of two Aspergillus fumigatus strains, ISSFT-021 and IF1SW-F4, isolated from HEPA filter debris and cupola surface of the ISS, respectively, is presented, along with a comparison to experimentally established clinical isolates Af293 and CEA10. In-depth analysis highlights variations in the proteome of both ISS-isolated strains when compared to the clinical strains. Proteins up-regulated in ISS isolates were involved in oxidative stress response, and carbohydrate and secondary metabolism. This report provides insight into possible molecular adaptation of filamentous fungi to the unique ISS environment. Lastly, an attempt was made to elucidate plausible causes of the enhanced virulence of both ISS-isolated A. fumigatus strains.

2019-01-09 | PXD008517 | Pride

Rpn4- and Proteasome- Mediated Yeast Response to Ethanol Stress: a View from a Proteome

Project description:Distilled spirits production using S. cerevisiae requires understanding the mechanisms of yeast cell response to the alcohol stress. Reportedly, specific mutations in genes of the ubiquitin-proteasome system, e.g. RPN4, may result in strains exhibiting either hyper-resistance or increased sensitivity to different alcohols. In this work, we studied Rpn4-dependent response of different yeast strains to short-term ethanol exposure. Three S. cerevisiae strains were used: wild-type (WT), mutant strain with RPN4 gene deletion (rpn4-delta), and mutant strain with decreased proteasome activity due to PRE1 deregulation (YPL). The resistance tests demonstrated an increased sensitivity of mutant strains to ethanol compared with WT. Comparative proteomics analysis revealed significant differences in molecular responses to ethanol between different strains. GO analysis of proteins upregulated in WT showed enrichments represented by oxidative and heat responses, protein folding/unfolding and protein degradation. Enrichment of at least one of these responses was not observed in mutant strains. At the same time, trehalose synthesis and accumulation of stress granules were enhanced in the mutant strains. We suggest that these pathways could partially compensate for the failure of ubiquitin-proteasome system to cope with the ethanol stress. Also, we suggest impaired compensatory activation of autophagic degradation system in rpn4-delta strain and propose that Rpn4 can be a regulator for autophagy upon ethanol stress. These findings can be a basis for creating genetically modified yeast strains resistant to high levels of alcohol, being further used for fermentation in ethanol production.

2020-04-22 | PXD014236 | Pride

Effect of acute ethanol on medidal prefrontal cortex across BXD genetic mapping panel and progenitors.

Project description:In order to elucidate the molecular mechanisms underlying individual variation in sensitivity to ethanol we profiled the prefrontal cortex transcriptomes of two inbred strains that exhibit divergent responses to acute ethanol, the C57BL6/J (B6) and DBA/2J (D2) strains, as well as 27 members of the BXD recombinant inbred panel, which was derived from a B6 x D2 cross. With this dataset we were able to identify several gene co-expression networks that were robustly altered by acute ethanol across the BXD panel. These ethanol-responsive gene-enriched networks were heavily populated by genes regulating synaptic transmission and neuroplasticity, and showed strong genetic linkage to discreet chromosomal loci. Network-based measurements of node importance identified several hub genes as established regulators of ethanol response phenotypes, while other hubs represent novel candidate modulators of ethanol responses.

2011-12-01 | GSE28515 | GEO

Gene expression profiling in control, heat-shock, and recovery treatment in an introgression line population of Caenorhabditis elegans L4 larvae

Project description:This experiment investigates the genetic architecture of gene expression (eQTL) in three different treatments in an N2xCB4856 introgression line population of Caenorhabditis elegans. The goal is to compare the effect of small CB4856 introgressions in an N2 genetic background versus a previously conducted experiment using recombinant inbred lines (RILs) derived from the same parental strains. We exposed ILs to a control (56 ILs), heat-stress (56 ILs), and recovery treatment (55 ILs). Additionally, also both parental strains, N2 and CB4856 were exposed to these three treatments (in at least 3 replicas per treatment). More specifically, these three conditions can be characterized as: (i) the control treatment was grown for 48 hours at 20C, (ii) the heat-stress treatment was grown for 46 hours at 20C followed by 2 hours at 35C, and (iii) the recovery treatment was grown for 46 hours at 20C, followed by 2 hours at 35C and thereafter 2 hours at 20C. Thereafter RNA was isolated, labelled and hybridized on microarray. The gene expression profiles were used for comparison versus findings in the RIL population (E-MTAB-5779).

2019-05-29 | E-MTAB-7424 | biostudies-arrayexpress

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