Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA113593 | ENA |
REPOSITORIES: ENA
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Project description:Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology. As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar cortices of 14 patients and six matched controls. A rigorous analysis pipeline was developed for analysis of digital gene expression studies. Sequences aligned to approximately 33,200 transcripts in each sample, with average coverage of 450 reads per gene. Following adjustments for confounding clinical, sample and experimental sources of variation, 215 genes differed significantly in expression between cases and controls. Golgi apparatus, vesicular transport, membrane association, Zinc binding and regulation of transcription were over-represented among differentially expressed genes. Twenty three genes with altered expression and involvement in presynaptic vesicular transport, Golgi function and GABAergic neurotransmission define a unifying molecular hypothesis for dysfunction in cerebellar cortex in SCZ.
2008-11-12 | GSE12297 | GEO
Project description:Schizophrenia (SCZ) is a common, disabling mental illness with high heritability but complex, poorly understood genetic etiology. As the first phase of a genomic convergence analysis of SCZ, we generated 16.7 billion nucleotides of short read, shotgun sequences of cDNA from post-mortem cerebellar cortices of 14 patients and six matched controls. A rigorous analysis pipeline was developed for analysis of digital gene expression studies. Sequences aligned to approximately 33,200 transcripts in each sample, with average coverage of 450 reads per gene. Following adjustments for confounding clinical, sample and experimental sources of variation, 215 genes differed significantly in expression between cases and controls. Golgi apparatus, vesicular transport, membrane association, Zinc binding and regulation of transcription were over-represented among differentially expressed genes. Twenty three genes with altered expression and involvement in presynaptic vesicular transport, Golgi function and GABAergic neurotransmission define a unifying molecular hypothesis for dysfunction in cerebellar cortex in SCZ. Experiment Overall Design: 16.7 billion nucleotides of shotgun, full length cDNA sequence data were generated using Illumina Genome Analyzer platforms with sequencing-by-synthesis (SBS) chemistry from 20 mRNA samples (Lister et al., 2008; Morin et al., 2008)(Mortazvi et al., 2008). mRNA samples were isolated post-mortem from the lateral hemispheres of the cerebellar cortices of 14 patients with SCZ and 6 control individuals (Paz et al., 2006; Bullock et al., In Press)(Table 1). Unrelated subjects were chosen to facilitate sampling of genetic heterogeneity (Freimer and Sabatti, 2004; McClellan et al., 2007). Cases and controls were approximately matched for age (cases, 45.2 + 11.8 years; controls 41.3 + 9.2 years), sex (all male), race, post-mortem interval (cases, 12.2 + 5.0 hours; controls 17.7 + 3.3 hours), cause of death, autopsy brain pH (cases, 6.54 + 0.19; controls 6.46 + 0.10) and RNA integrity number (cases, 8.06 + 0.53; controls, 7.87 + 0.41) (Table 1). 12.5 – 38.7 million, high quality sequences of length 32 – 36 bp were generated per sample (Table 2). Sequences were aligned to the human genome and RefSeq transcript databases using the algorithm GMAP, which allowed < 2 (< 6%) mismatches (Wu and Watanabe, 2005). There was little intra-sample variability in the number of sequences aligned to each locus from run-to-run or instrument-to-instrument (Fig. 1A; all source coefficient of variation 3.4%). 43.5 + 6.7% of sequences aligned to a transcript and 69.4 + 9.6% to the genome, evidence that annotation of mRNA isoforms in Homo sapiens is incomplete (Birney et al., 2007) (Table 2). 91% of alignments were unique (Table 2). Reads aligning to more than one location contained repetitive, paralogous, polymorphic or low complexity sequences and primarily mapped to untranslated regions or highly polymorphic gene families, such as major histocompatibility genes (Sugarbaker et al., 2008). Unmapped sequences did not align to mitochondrial or 1879 viral genomes, offering negative evidence of chronic viral etiology for SCZ in these patients.
2009-08-29 | E-GEOD-12297 | biostudies-arrayexpress
Project description:RNA-Seq was performed in post-mortem SCA1 cerebellum at the end stage of the disease and an age/sex-matched control tissue from a healthy individual.
2020-02-18 | E-MTAB-7714 | biostudies-arrayexpress
Project description:RNA-seq evaluation of enriched Purkinje cells from the post-mortem human cerebellum. Purkinje cells were removed via laser capture microdissection and pooled for RNA-extraction and sequencing. 24 ET patients and 16 controls healthy age matched were compared.
2023-02-28 | GSE197345 | GEO
Project description:Post mortem human brain tissue comparison between HD patients and controls from 3 brain regions - cerebellum, frontal cortex [BA4, BA9] and caudate nucleus. Gene expression analysed using linear models from LIMMA package in Bioconductor suite. Keywords: disease state analysis
2006-02-08 | GSE3790 | GEO
Project description:Evaluating RNA quality and transcriptomic profile of beef muscle tissue over time post-mortem may provide insight on RNA degradation and underlying biological and functional mechanisms influencing the biochemical changes occurring post-mortem that transform muscle tissue to meat. RNA-sequencing was performed on longissimus thoracis et lumborum (LTL) muscle samples collected at 5 time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from British Continental crossbred beef heifers (n=7). Processed mRNA reads were aligned to the ARS-UCD1.2 bovine genome assembly. Differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend of both up and downregulated genes increasing over time . Gene ontology and KEGG pathway term enrichment analyses revealed significant enrichment of biological and molecular functions relating to cellular energy, oxidative stress and NADH activity specific to early time points, as well as cellular signaling and transport and ribosome activity at specific to late time points. This study also revealed that LTL muscle tissue samples, collected as late as 72 h post-mortem remained at a high RNA integrity, suggesting opportunities for late sampling regimes for RNA-Seq analysis of post-mortem muscle tissue and the potential for larger studies to associate desirable meat quality traits with post-mortem transcriptome activity. Additionally, this study highlights the need to evaluate non-coding genetic features involved with epigenetic regulation in post-mortem muscle tissue, as indicated by non-coding RNA transcripts detected post-mortem, including small nucleolar RNA, mitochondrial DNA genes, and long non-coding RNA.
2021-06-02 | GSE163766 | GEO
Project description:Astrotactin 2 (ASTN2) is a transmembrane, neuronal protein that functions in receptor trafficking and modulates cerebellar Purkinje cell (PC) synaptic activity. We recently reported a family with a paternally inherited intragenic ASTN2 duplication, with a range of neurodevelopmental disorders, including autism spectrum disorder (ASD), learning difficulties and speech and language delay. To provide a genetic model for the role of the cerebellum in ASD-related behaviors and study ASTN2 role in cerebellar circuit function, we generated global and Purkinje cell-specific conditional Astn2 knockout (KO and cKO, respectively) mouse lines. Astn2 KO mice exhibit strong ASD-related behavioral phenotypes, including a marked decrease in separation-induced pup ultrasonic vocalization (USV) calls, increased hyperactivity and repetitive behaviors, altered social behaviors, and impaired cerebellar-dependent eyeblink conditioning. Increased hyperactivity and repetitive behaviors were also prominent in Astn2 cKO animals. By Golgi staining, Astn2 KO PCs have region-specific changes in dendritic spine density and filopodia numbers. Proteomic analysis of Astn2 KO cerebellum reveals a marked upregulation of ASTN2 family member, ASTN1, a neuron-glial adhesion protein. Immunohistochemistry and electron microscopy demonstrates a large increase in Bergmann glia volume in the molecular layer of Astn2 KO animals. Electrophysiological experiments indicate a reduced frequency of spontaneous EPSCs, as well as increased amplitudes of both spontaneous EPSCs and IPSCs in the Astn2 KO animals, suggesting that pre- and post-synaptic components of synaptic transmission are altered. Thus, ASTN2 regulates ASD-like behaviors and cerebellar circuit properties.
2024-03-07 | GSE254224 | GEO
Project description:AMPA receptors (AMPARs) are multimodal transducers of glutamatergic signals throughout the brain. Their diversity is exemplified in the cerebellum, the brain structure integrating sensorimotor information. At afferent synapses, AMPARs mediate high-frequency excitation, while in Bergmann glia (BG) they support slow calcium transients that modulate synaptic transmission. This spectrum arises from different combinations of core subunits (GluA1-4), auxiliary proteins, and post-transcriptional modifications. Here, using mass-spectrometry, cryo-EM, and electrophysiology, we characterize major cerebellar AMPARs: low calcium-permeable GluA2/A4 heteromers with four TARP subunits, mainly neuronal in origin, and BG-specific calcium-permeable GluA1/A4 heteromers containing only two Type-2 TARPs. Moreover, GluA4 receptors consistently exhibit compact N-terminal domains that promote synaptic delivery. Our study defines the organisational principles of native AMPAR complexes in the mammalian cerebellum and reveals how different receptor subtypes support cell-type specific functions.
2026-02-26 | PXD069620 | Pride
Project description:Multiomics Analyses of Vesicular Transport Pathway-Specific Transcripts and Proteins in Ovine Amnion: Responses to Altered Intramembranous Transport
| PRJNA529913 | ENA
Project description:MK-801, a non-competitive NMDA receptor (NMDAR) antagonist, disturbs NMDAR function in rodents and induces psychological and behavioral changes similar to schizophrenia(SCZ). However, the effects of MK-801 treatment on gene expression in prefrontal cortex (PFC) are largely unknown. We have established MK-801 animal models to explore the etiology and pathophysiology of schizophrenia. Transcriptome analysis of the prefrontal cortex reveals that the differentially expressed genes mainly aggregate in chemical synaptic transmission and immune system process. Gene association patterns which are involved in synaptic vesicle cycle and mitochondrial electron transport chain have also been altered. Together, these observations underscore that dysfunction in glutamatergic synaptic vesicle cycle and mitochondrial electron transport chain has an impact on the pathogenesis of SCZ.
2019-03-12 | GSE111708 | GEO