GNPS Stein Schizophrenia and aging study
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
Tanya T. Nguyen
PROVIDER: MSV000087612 | GNPS | Thu Jun 10 17:57:00 BST 2021
REPOSITORIES: GNPS
Similar Datasets
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment studies the response of gene expression in roots of 25-35 day old plants grown on hydroponics after 6, 48 and 96 hours of potassium starvation. RNA from roots was extracted after transfer to control (control) or potassium free nutrient solution respectively (starvation). Experimenter name = Julian Schroeder Experimenter phone = 619-534-7759 Experimenter fax = 619-534-7108 Experimenter department = J Schroeder Laboratory Experimenter institute = University of California-San Diego Experimenter address = Biology Department Experimenter address = University of California-San Diego Experimenter address = La Jolla Experimenter zip/postal_code = CA 92093-0116 Experimenter country = USA Keywords: time_series_design; growth_condition_design
2007-01-08 | GSE5744 | GEO
Project description:This experiment was annotated by TAIR (http://arabidopsis.org). This experiment studies the response of gene expression in roots of 25-35 day old plants grown on hydroponics after 6, 48 and 96 hours of potassium starvation. RNA from roots was extracted after transfer to control (control) or potassium free nutrient solution respectively (starvation). Experimenter name = Julian Schroeder; Experimenter phone = 619-534-7759; Experimenter fax = 619-534-7108; Experimenter department = J Schroeder Laboratory; Experimenter institute = University of California-San Diego; Experimenter address = Biology Department; Experimenter address = University of California-San Diego; Experimenter address = La Jolla; Experimenter zip/postal_code = CA 92093-0116; Experimenter country = USA Experiment Overall Design: 4 samples were used in this experiment
2008-06-14 | E-GEOD-5744 | biostudies-arrayexpress
Project description:Please Note, if a password is required, please try "a", the generic password for Massive.
These data are in support of the manuscript:
Post-translational Modifications of Endogenous Tau in Wildtype and Human Amyloid Precursor Protein Transgenic Mice
Meaghan Morris*a,b, Giselle M. Knudsen*c, Sumihiro Maedaa,d, Jonathan C. Trinidadc, Alexandra Ianoviciuc, Alma L. Burlingamec, Lennart Muckea,d
aGladstone Institute of Neurological Disease, San Francisco, California 94158, USA
bBiochemistry, Cellular and Molecular Biology Graduate Program, Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
cMass Spectrometry Facility, Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, USA
dDepartment of Neurology, University of California, San Francisco, California 94158, USA
*These authors contributed equally to this work
2014-07-30 | MSV000078796 | MassIVE
Project description:Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex-chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. Experimental design: Two groups of male control subjects and female control subjects were selected that had no history of psychiatric disorder. Each subject was analyzed by microarray in 3 brain regions: AnCg (anterior cingulate cortex), DLPFC (dorsalateral prefrontal cortex), and CB (cerebellum). Total RNA aliquots for some subjects were analyzed at either 1 site, 2 sites, or 3 sites (UM , University of Michigan); UCD (University of California, Davis); or UCI (University of California, Irvine). The data was analyzed by looking at each Male vs Female comparison separately at each site by a t-test for gender differences. Thus for one brain region, a Male vs Female comparison was run at 3 sites, and the overlapping significant genes from the three comparisons were reported. We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications. Keywords: other
2005-01-28 | GSE2164 | GEO
Project description:Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex-chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences. Experimental design: Two groups of male control subjects and female control subjects were selected that had no history of psychiatric disorder. Each subject was analyzed by microarray in 3 brain regions: AnCg (anterior cingulate cortex), DLPFC (dorsalateral prefrontal cortex), and CB (cerebellum). Total RNA aliquots for some subjects were analyzed at either 1 site, 2 sites, or 3 sites (UM , University of Michigan); UCD (University of California, Davis); or UCI (University of California, Irvine). The data was analyzed by looking at each Male vs Female comparison separately at each site by a t-test for gender differences. Thus for one brain region, a Male vs Female comparison was run at 3 sites, and the overlapping significant genes from the three comparisons were reported. We appreciate the assistance of Richard Stein, Ph.D. and Preston Cartagena, Psy.D. for their contributions to postmortem clinical characterization of subjects. We acknowledge Kathleen Burke as well as Jacque Berndt and the investigators and medical examiners at the Orange County Coroners Office for procurement of brain tissue. We also appreciate the technical contributions of Kevin Overman, Sharon Burke, and Phong Nguyen. F. Warren Lovell, M.D, performed a neuropathological evaluation of the postmortem brains. Tissue specimens were processed and stored at the Human Brain and Spinal Fluid Resource Center, Veteran's Medical Center, Los Angeles under the direction of Wallace W. Tourtellotte, M.D., Ph.D. This project is supported by the NIMH Conte Center Grant P50 MH60398, Pritzker Neuropsychiatric Disorders Research Consortium, William Lion Penzner Foundation (UCI), Della Martin Foundation (UCI), NIMH Grant #MH54844 (EGJ), W.M. Keck Foundation (EGJ), and the NIMH Program Project MH42251 (SJW and HA). The authors are members of of a Conte Center supported by the NIMH and the Pritzker Neuropsychiatric Disorders Research Consortium, which is supported by the Pritzker Neuropsychiatric Disorders Research Fund L.L.C. A shared intellectual property agreement exists between this philanthropic fund and the University of Michigan, the University of California, and Stanford University to encourage the development of appropriate findings for research and clinical applications.
2008-06-12 | E-GEOD-2164 | biostudies-arrayexpress
Project description:We measured gene expression in the adrenal glands of the Spontaneously Hypertensive Rat (SHR) and Wistar-Kyoto rat (WKY) using Affymetrix RG-U34A GeneChips. All rats were aged-matched at 4-weeks. The rats were obtained from the colonies at the Univeristy of California San Diego, La Jolla, CA. Keywords: other
2004-11-02 | GSE1675 | GEO
Project description:Interlab Study of LC-MS/MS analyis of Marine Dissolved Organic Matter from SIO Pietr (San Diego, California, USA) and algae extracts, extracted via PPL SPE
2022-02-11 | MSV000088823 | MassIVE
Project description:Methods: The DNT cells incubation with anti-CD3/CD28 antibodies were stimulated with UDCA (60uM) for 48 hours, then transcriptome sequencing studies were performed on DNT cells RNA.Transcriptome sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and sequenced on an Illumina Hiseq platform (Illumina, San Diego, CA). Sequences were aligned to the reference genome with TopHat and processed with Cufflinks, which quantifies each transcript in each sample using reference annotations produced by the University of California Santa Cruz UCSC. Differentially expressed genes with a fold change of >=1.41 and pvalue <= 0.05 between UDCA treated and control DNT cells were submitted to GO and KEGG enrichment analysis, which uses unbiased methods to assess pathway enrichment.
2022-02-28 | GSE167116 | GEO
Project description:Endovascular biopsy and fluorescence activated cell sorting was used to enrich for viable endothelial cells (ECs) from a vertebrobasilar aneurysm and the femoral artery. scRNAseq was then performed on 24 aneurysmal endothelial cells and 23 patient-matched non-aneurysmal femoral artery endothelial cells. cDNA libraries were prepared using the Smart-seq2 protocol on a Fluidigm C1 system (Fluidigm, South San Francisco, California) and sequenced on a HiSeq2500 machine (Illumina, San Diego, California).
2021-07-01 | E-MTAB-10681 | biostudies-arrayexpress
Project description:Analysis of CD4+ T cell gene expression changes after 4 and 24 weeks of Maraviroc administration relative to baseline in 25 immunodiscordant patients with viral suppression. Maraviroc elicited very modest changes in CD4+ T cell transcriptome. The goal of this study was to identify genes with a potential role in Maraviroc-induced CD4+ T cell recovery in immunodiscordant patients. The study measured gene expression in CD4+ T cells isolated from the whole blood of HIV-infected patients before and at two time points after addition of Maraviroc to the baseline antiretroviral therapy. Thirty two patients were recruited from 3 sites, University of California, San Diego (UCSD), University of California, Los Angeles (UCLA) and University of Southern California (USC), and peripheral blood samples were obtained at 3 visits, week 0 (baseline), week 4 and week 24 after initiation of Maraviroc therapy. Because of poor RNA quality and outliers on the microarrays, 7 patients were excluded from the study. Non-outlier week 0 and week 24 arrays from one of the patients (Patient ID 01-005) were used for array data normalization and processing, but were not included in the time course analysis since the week 4 sample was not available.
2014-04-16 | E-GEOD-56804 | biostudies-arrayexpress