Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

31 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of mouse brain regions (bed nucleus of the stria terminalis, hippocampus, hypothalamus, periaqueductal gray, and pituitary gland) in six mouse strains (129S6/SvEvTac, A/J, C57BL/6J, C3H/HeJ, DBA/2J, and FVB/NJ)

ABSTRACT: Gene expression patterns were determined from five brain regions (bed nucleus of the stria terminalis, hippocampus, hypothalamus, periaqueductal gray, and pituitary gland) in six mouse strains (129S6/SvEvTac, A/J, C57BL/6J, C3H/HeJ, DBA/2J, and FVB/NJ). At least two replicate samples per brain region/strain were analyzed using Affymetrix Mouse Genome 430 2.0 arrays. Experiment Overall Design: six mouse strains and five brain regions were analyzed

ORGANISM(S): Mus musculus

SUBMITTER: Carrolee Barlow

PROVIDER: E-GEOD-4734 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

DNA variation and brain region-specific expression profiles exhibit different relationships between inbred mouse strains: implications for eQTL mapping studies.

Hovatta Iiris I Zapala Matthew A MA Broide Ron S RS Schadt Eric E EE Libiger Ondrej O Schork Nicholas J NJ Lockhart David J DJ Barlow Carrolee C

Genome biology 20070101 2

<h4>Background</h4>Expression quantitative trait locus (eQTL) mapping is used to find loci that are responsible for the transcriptional activity of a particular gene. In recent eQTL studies, expression profiles were derived from either homogenized whole brain or collections of large brain regions. However, the brain is a very heterogeneous organ, and expression profiles of different brain regions vary significantly. Because of the importance and potential power of eQTL studies in identifying reg ...[more]

PMID: 17324278

Similar Datasets

Transcription profiling of different regions of mouse brain to study adult mouse gene expression patterns in common strains.

Project description:Adult mouse gene expression patterns in common strains. Experiment Overall Design: six mouse strains and seven brain regions were analyzed

2007-09-14 | E-GEOD-3327 | biostudies-arrayexpress

Transcription profiling of rat lumbar spinal cord following ventral root avulsion in two inbred strains to investigate susceptibility to neurodegeneration

Project description:Gene expression profiling in rat lumbar spinal cord following ventral root avulsion in the two inbred rat strains.

2006-08-15 | E-MEXP-671 | biostudies-arrayexpress

The clock transcription factor BMAL1 is a key regulator of extracellular matrix homeostasis and cell fate in the intervertebral disc

Project description:The circadian clock in mammals temporally coordinates physiological and behavioural processes to anticipate daily rhythmic changes in their environment. Chronic disruption to circadian rhythms (e.g., through ageing or shift work) is thought to contribute to a multitude of diseases, including degeneration of the musculoskeletal system. The intervertebral disc (IVD) in the spine contains circadian clocks which control ~6% of the transcriptome in a rhythmic manner, including key genes involved in extracellular matrix (ECM) homeostasis. However, it remains largely unknown to what extent the local IVD molecular clock is required to drive rhythmic gene transcription and IVD physiology. In this work, we identified profound age-related changes of ECM microarchitecture and an endochondral ossification-like phenotype in the annulus fibrosus (AF) region of the IVD in the Col2a1-Bmal1 knockout mice. Reported here is the circadian time series RNA-Seq of the whole IVD in Bmal1 knockout mice.

2023-08-17 | E-MTAB-13083 | biostudies-arrayexpress

Quantitative LC-MS/MS Proteomics of human small intestine

Project description:The objective was to determine the expression of a wide range proteins pertinent to metabolism and disposition of chemicals and nutrients in the intestinal epithelium. Ileum and jejunum biopsy specimens were obtained from 16 patients undergoing gastrointestinal elective surgery. Mucosal fractions were prepared and analysed using targeted and global proteomic approaches. A total of 29 enzymes, 32 transporters, 6 tight junction proteins, 2 adhesion proteins, alkaline phosphatase, thioredoxin, 5 markers and 1 regulatory protein were quantified; 60 for the first time.

2021-09-09 | PXD020987 | Pride

Comprehensive proteome of the adult neural stem cell niche identifies key regulators of adult neurogenesis

Project description:Neural stem cells (NSCs) generating new neurons are restricted to few niches in the adult mammalian brain, while the remainder rather promotes gliogenesis. Here we take advantage of the spatial separation of an NSC niche (the subependymal zone) and the region to where the newly generated neurons migrate and integrate (the olfactory bulb). Using state-of-the-art mass spectrometry we present a comprehensive proteomic characterization of these niches compared to a region of the normal brain parenchyma (cerebral cortex) that is not contusive to neurogenesis and new neuron integration. We find unique compositions of regulatory ECM components in the neurogenic niche, with quiescent NSCs as a main source of their local ECM, including the multi-functional enzyme transglutaminase 2 that we identify as crucial for neurogenesis. Atomic force microscopy further corroborates indications from the proteome that neurogenic niches are significantly stiffer than the non-neurogenic parenchyma, highlighting the unique properties of these special niches.

2020-01-27 | PXD016632 | Pride

Phosphoproteomics of C.elegans RNA binding protein mutants

Project description:Nonsense-mediated mRNA decay (NMD) monitors the quality of transcriptomes and degrades messenger RNAs containing splicing errors or premature stop codons. NMD thus dictates the severity and outcome of genetic disorders, gene edits and knockouts as well as the prevalence of neoantigens. Central to the NMD pathway are SMG-1, an ATM/ATR-like kinase, and its downstream target SMG-2/UPF1, a highly processive DNA/RNA helicase. Interestingly, many NMD factors acquired additional ‘moonlighting’ functions in the nucleus, including roles in DNA synthesis and DNA damage signalling. While having the same protein controlling RNA and DNA metabolism could be beneficial, it could also lead to signalling conflicts that jeopardize genome stability. Surprisingly little is known about the incidence and impact of such crosstalk in biology, neither in physiological nor in pathological scenarios. Here, via genetics screens and genome-wide analyses, we identified unforeseen crosstalk between RNA surveillance and DNA repair in living animals. Defects in RNA processing, due to viable THO complex or PNN-1 mutations, trigger SMG-1 activity, which causes a major shift in DNA repair and compromises genome stability in somatic tissues. Mechanistically, we find SMG-1 and SMG-2/UPF1, but not NMD per se, to suppress DNA repair by classical non-homologous end-joining while allowing mutagenic repair by single strand annealing. We postulate that aberrant RNA structures trigger crosstalk that re-directs DNA repair and genome evolution.

2022-08-12 | PXD022616 | Pride

Identification of early neurodegenerative pathways in progressive multiple sclerosis

Project description:Progressive multiple sclerosis (MS) is characterized by unrelenting neurodegeneration, which causes cumulative disability and is refractory to current treatments. Drug development to prevent disease progression is an urgent clinical need yet is constrained by an incomplete understanding of its complex pathogenesis. Using spatial transcriptomics and proteomics on fresh-frozen human MS brain tissue, we identified multicellular mechanisms of progressive MS pathogenesis and traced their origin in relation to spatially distributed stages of neurodegeneration. By resolving ligand–receptor interactions in local microenvironments, we discovered defunct trophic and anti-inflammatory intercellular communications within areas of early neuronal decline. Proteins associated with neuronal damage in patient samples showed mechanistic concordance with published in vivo knockdown and central nervous system (CNS) disease models, supporting their causal role and value as potential therapeutic targets in progressive MS. Our findings provide a new framework for drug development strategies, rooted in an understanding of the complex cellular and signaling dynamics in human diseased tissue that facilitate this debilitating disease.

2022-06-05 | PXD026529 | Pride

Hypothalamic gene expression profile indicates a reduction in G-protein signaling in the wfs1 mutant mice

Project description:WFS1 gene is coding protein with unknown function but its functional deficiency causes different neuropsychiatric and neuroendocrine syndromes. In the present study we aimed to find the functional networks influenced by the Wfs1 deficiency in the hypothalamus. We performed gene expression profiling (Mouse Gene 1.0 ST Arrays) in Wfs1 deficient mice (ko). Modified t-statistics was used for comparison of groups (wt vs ko). Functional annotation of the alterations in RNA levels was performed with Ingenuity Pathway Analysis. 305 genes were differentially expressed with nominal p-value less than 0.01. FDR adjusted p-values were significant (0.007) only for two genes M-bM-^@M-^S C4b (t=9.66) and Wfs1 (t=-9.03). However, several genes related to the G-protein signalling were very close to the FDR adjusted significance. For instance, Rgs4 (regulator of G-protein signalling 4) was down-regulated (-0.34, t=-5.4) in Wfs1 deficient mice. Changes in Rgs4 and C4B expression were confirmed by QRT-PCR. In humans, Rgs4 is in the locus for bipolar disease (BPD) and its expression is down-regulated in BPD. C4b is the gene related to the neurodegenerative diseases. In conclusion, hypothalamic gene expression profiling indicates alterations in some functionally relevant molecular pathways explaining the clinical syndrome in the Wolfram syndrome patients. 18 samples, two genotypes (wild type and mutant), in 129S6 genetic background

2011-11-02 | E-GEOD-33372 | biostudies-arrayexpress

Expression data from junctional zone of placenta in Brown Norway and Holtzman-Sprague Dawley rat strains at gestation day 18.5

Project description:Placentation differs in the BN rat strain when compared to HSD and DSS rat strains. Intrauterine trophoblast invasion is shallow and the junctional zone is underdeveloped in the BN rat. These structural differences are striking but their quantification is not conducive to high throughput analyses. In the rat, the junctional zone can be readily dissected and is more homogenous than other components of the placentation site. HSD and BN rat gestation day 18.5 junctional zone gene expression profiles were determined using DNA microarray analysis to identity placenta-associate quantitate traits. Total RNAs from Junctional zone tissues of gestation day18.5 HSD and BN rat strains were subjected to microarray analyses. Three biological replicates of each strains were analyzed.

2011-05-13 | E-GEOD-29247 | biostudies-arrayexpress

Gene expression profiling of temporal lobes of wfs1 deficient mice

Project description:Aim of present study was to describe the changes induced deletion of the Wfs1 gene in the temporal lobe of mice. Mutant mice were backcrossed to two different genomic backgrounds in order to exclude confounding foreign genomic background influence. Samples from temporal lobes were analyzed by using Affymetrix Genechips, expression profiles were functionally annotated by using GSEA and Ingenuity Pathway Analysis. We found that Wfs1 mutant mice are significantly smaller (20.9 +/- 1.6 g) than their wild-type counterparts (31.0 +/- 0.6 g, p < 0.0001). Interestingly, genechip analysis identified growth hormone transcripts up-regulated and functional analysis found appropriate pathways activated. Moreover, we found significant increase in the level of IGF1 in the plasma of wfs1 mutant mice. Taken together, wfs1 mutation induces growth retardation whereas the growth hormone pathway is activated. Further studies are needed to describe biochemical and molecular details of the growth hormone axis in the wfs1 mutant mice. 37 samples, two genotypes (wild type and mutant), in two different genetic background (C57B6 and 129S6)

2010-04-06 | E-GEOD-15293 | 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