Expression profiling of adult mouse brain and liver tissues (RNA-seq)
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2500
ORGANISM(S): Mus musculus
SUBMITTER: I-Hsuan Lin
PROVIDER: E-MTAB-5166 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:5-hydroxymethylcytosine (5hmC) is the first oxidative product of the TET-mediated 5-methylcytosine (5mC) demethylation pathway. It is a key intermediate in cytosine demethylation, and have potential regulatory functions with emerging importance in mammalian biology. In this work, we used a chemical capture-based technique that coupled with next-generation sequencing to investigate the global 5hmC methylation in five brain subregions (cerebellum, cortex, hippocampus, hypothalamus and thalamus) and liver tissues from female and male adult mice. We also performed total RNA sequencing to study the association between 5hmC and gene expression. The enriched 5-hmC library was sequenced on a HiSeq2500 by paired-end sequencing with 100 bp read length.
2017-01-31 | E-MTAB-5167 | biostudies-arrayexpress
Project description:The thalamus of the brain acts as a relay station; taking inputs from several parts of the brain and then sending the information to the cortex and vice versa. It is also the structure know to affected in several brain developmental disorders such as schizophrenia, autism spectrum disorders, bipolar disorders etc. Upon in situ hybridisation one can visualise the expression of the transcription factor Tcf7l2 to be highest in prosomeric regions of the thalamus throughout development. With this information in mind we set out to find out, if the expression of Tcf7l2 is essential for the identity of the thalamic structure. Therefore, Tcf7l2 was knocked (KO) out using Cre+mice at embryonic stage E18.5 and postnatal adult stage P60. The E18.5 Tcf7l2 KO is a total knockout and the P60 Tcf7l2 KO is neuron-specific knockout. Total RNA was extracted and sent for sequencing using Illumina 2500. The data obtained was aligned by HISAT2 alignment tool, and the excon read counts were gathered using htseq counts, and expression normalization and differential gene expression was analysed using DESeq2.
2020-02-10 | E-MTAB-8755 | biostudies-arrayexpress
Project description:G72 transgenic (TG, transgenic mice carrying the G72/G30 locus) and wildtype (WT) mice with a CD1 background were used for transcriptome data acquisition. Importantly, three different brain regions, i.e., the retrosplenial cortex, the hippocampus and thalamus, of animals from both sexes were investigated. In total, eight WT control animals (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.46 ± 0.11 wks) and eight G72 transgenic mice (four ♂, age: 23.14 ± 0.00 wks; four ♀, age: 23.14 ± 0.00 wks) were used for dissection of the cortex, thalamus and hippocampus for subsequent transcriptome analysis. Our data allow new insight into relevant alterations in gene transcript levels in G72 mice and allow the reader/user to carry out additional complex analyses to characterize potential sex-, age- and brain-region-specific profiles in gene expression and related pathways. These analyses could trigger biomarker identification and drug research and development in schizophrenia research in the future.
2023-12-01 | E-MTAB-13547 | biostudies-arrayexpress
Project description:Rheumatoid arthritis (RA) is linked to depression and dementia in later life by inflammatory involvement of the central nervous system (CNS). Regional heterogeneity of brain immunophenotypes was described under homeostasis, but a topographical resolution of CNS immune responses in chronic peripheral inflammatory diseases like RA is missing. We demonstrate regional heterogeneity of CNS susceptibility to chronic peripheral inflammation in the human tumor necrosis factor α transgenic (TNFtg) mouse model of RA. TNFtg mice showed myeloid cell infiltration, microglial activation, and a mutual transcriptomic fingerprint of neuroinflammation in the cortex, striatum, and thalamus. Immune responses were minimal in the hippocampus and cerebellum. We demonstrate regional CNS immune responses to chronic peripheral inflammation, sparing the hippocampus and cerebellum and reversible by peripheral anti-inflammatory treatment. Targeting microenvironmental susceptibility or resilience of brain regions will help to prevent and treat RA-related neuropsychiatric comorbidity. RNA-sequencing was performed from five brain regions (cortex, striatum, thalamus, hippocampus, and cerebellum) from C57Bl6/J wild type mice and TNFtg mice (strain Tg197; kindly provided by George Kollias (Fleming Institute, Vari, Greece).
2018-10-22 | E-MTAB-7279 | biostudies-arrayexpress
Project description:Fatal familial insomnia (FFI) is a special subtype of genetic human prion diseases that is caused by the D178N mutation of the prion protein gene (PRNP). In this study, global expression patterns of the thalamus and parietal cortex from three patients with FFI were analyzed by Affymetrix Human Genome U133+ 2.0 chip. We used microarrays to detail the global gene expression in tissues from normal human and FFI patients thalamus, or parietal lobe. Tissues from normal human and FFI patients' thalamus, or parietal lobe were for RNA extraction and hybridization on Affymetrix microarrays.
2015-08-30 | E-GEOD-40562 | biostudies-arrayexpress
Project description:Transcriptional profiling of rat hippocampus comparing rats subjected to chronic (1 hour daily during 14 days) vetrolateral thalamus stimulation (DBS group) with sham operated rats (with electrode placement but without stimulation) and with naive rats. Three-condition experiment, DBS, sham and naive. Every sample consisted of pooled hippocampi from three rats. Slices between Bregma levels -2 and -4 were used for dissections of the hippocampi. Common reference design, comparing every condition versus a brain pooled tissue consisting of pooled hippocampal, thalamic and cortical brain tissue of the naive (n=4), sham-operated (n=5) and stimulated (n=4) rats. Biological replicates: 4 DBS, 4 sham and 3 naive. One replicate per array. Deep brain stimulation
2011-06-30 | E-GEOD-25860 | biostudies-arrayexpress
Project description:Conscious awareness of breathing requires the activation of higher brain centers. The sensation of breathing is believed to be a neural gating process. The thalamus provides the brain structure that could be responsible for the gating of respiratory sensory information to the cortex. It was reasoned that if the thalamus is the neural gate, then tracheal obstructions will modulate the gene expression profile of the thalamus. Anesthetized rats were instrumented with an inflatable cuff sutured around the trachea. The cuff was inflated to obstruct 2-4 breaths, then deflated for a minimum of 15 breaths. The obstructions were repeated for 10 min followed by immediate brain removal, and the medial thalamus was dissected and prepared for microarray analysis. Gene expression profiles were measured using Agilent Technology Oligo Microarrays. Following the occlusion protocol, 588 genes were found to be altered (p < 0.05, log2 fold change ≥ 0.4), with 327 down-regulated and 261 genes up-regulated. A significant up-regulation of the serotonin HTR2A receptor and significant down-regulation of the dopamine DRD1 receptor genes were found. A pathway analysis was performed targeting serotonin and dopamine receptor pathways. The mitogen activated protein kinase 1 (MAPK1) gene was significantly down-regulated. MAPK1 is an inhibitory regulator of the serotonin HTR2A receptor and facilitatory regulator for the dopamine DRD1 receptor. Down-regulation of MAPK1 may be related to the 2-fold up-regulation of HTR2A and 2-fold down-regulation of DRD1 suggesting an interaction in the medial thalamus serotonin-dopamine pathway elicited by airway obstruction. These results demonstrate an immediate change in gene expression in thalamic arousal-fear-anxiety-motivation related serotonin and dopamine receptors in response to airway obstruction. The results support the hypothesis that the thalamus is a component in the respiratory mechanosensory neural pathway. Four experimental animals that received tracheal occlusions and four surgical control animals were used. A reference design was used to compare all samples.
2010-11-05 | E-GEOD-25153 | biostudies-arrayexpress
Project description:Background: Microorganisms are the major cause of food spoilage during storage, processing and distribution. Pseudomonas fluorescens is a typical spoilage bacterium that contributes to a large extent to the spoilage process of proteinaceous food. RpoS is considered an important global regulator involved in stress survival and virulence in many pathogens. Our previous work revealed that RpoS contributed to the spoilage activities of P. fluorescens by regulating resistance to different stress conditions, extracellular acylated homoserine lactone (AHL) levels, extracellular protease and total volatile basic nitrogen (TVB-N) production. However, RpoS-dependent genes in P. fluorescens remained undefined. Results: RNA-seq transcriptomics analysis combined with quantitative proteomics analysis basing on multiplexed isobaric tandem mass tag (TMT) labeling was performed for the P. fluorescens wild-type strain UK4 and its derivative carrying a rpoS mutation. A total of 375 differentially expressed genes (DEGs) and 212 differentially expressed proteins (DEPs) were identified in these two backgrounds. The DGEs were further verified by qRT-PCR tests, and the genes directly regulated by RpoS were confirmed by 5’-RACE-PCR sequencing. The combining transcriptome and proteome analysis revealed a role of this regulator in several cellular processes, including polysaccharide metabolism, intracellular secretion and extracellular structures, cell well biogenesis, stress responses, ammonia and biogenic amine production, which may contribute to biofilm formation, stress resistance and spoilage activities of P. fluorescens. Moreover, in this work we indeed observed that RpoS contributed to the production of the macrocolony biofilm’s matrix.
2019-11-12 | PXD010845 | Pride
Project description:The thalamus may be the critical brain area involved in sensory gating and the relay of respiratory mechanical information to the cerebral cortex for the conscious awareness of breathing. We hypothesized that respiratory mechanical stimuli in the form of tracheal occlusions would modulate the gene expression profile of the thalamus. Specifically, it was reasoned that conditioning to the respiratory loading would induce a state change in the medial thalamus consistent with a change in sensory gating and the activation of molecular pathways associated with learning and memory. In addition, respiratory loading is stressful and thus should elicit changes in gene expressions related to stress, anxiety, and depression. Rats were instrumented with inflatable tracheal cuffs. Following surgical recovery, they underwent ten days (5 days/week) of transient tracheal occlusion conditioning. On day 10, the animals were sacrificed and the brains removed. The medial thalamus was dissected and microarray analysis of gene expression performed. Tracheal obstruction conditioning modulated a total of 661 genes (p < 0.05, log2 fold change ≥ 0.58), 250 genes were down-regulated and 411 up-regulated. There was a significant down-regulation of GAD1, GAD2 and HTR1A, HTR2A genes. CCK, PRKCG, mGluR4, and KCJN9 genes were significantly up-regulated. Some of these genes have been associated with anxiety and depression, while others have been shown to play a role in switching between tonic and burst firing modes in the thalamus and thus may be involved in gating of the respiratory stimuli. Furthermore, gene ontology and pathway analysis showed a significant modulation of learning and memory pathways. These results support the hypothesis that the medial thalamus is involved in the respiratory sensory neural pathway due to the state change of its gene expression profile following repeated tracheal occlusions. Four experimental animals that received tracheal occlusions and four surgical control animals were used. A reference design was used to compare all samples.
2010-11-05 | E-GEOD-25152 | biostudies-arrayexpress
Project description:Molecular mechanisms controlling specification and differentiation of distinct neuron subtypes in the cerebral cortex are not well understood. Corticothalamic projection neurons (CThPN) are a diverse set of neurons, critical for function of the neocortex, but little is known about the molecular mechansims controlling their development. We used microarrays to detail CThPN gene expression at 3 developmental time points. We then compared CThPN gene expression, with the gene expression of other neuron subtypes in the cerebral cortex at the same stages (previously described in Arlotta et a., 2005) CThPN were retrogradely label with fluorescent microespheres injected into the thalamus, and were FACS purified at 3 developmental stages for RNA extraction and hybridization on Affymetrix microarrays.
2016-06-28 | E-GEOD-61711 | biostudies-arrayexpress