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Proteomics analyses of dexamethasone-treated PB and CB erythroid progenitors
Internal Dataset- Authors
- Ryan AshleyHongxia YanNan WangJohn Hale14 more author(s)...
- Description
Biological triplicates of peripheral blood (PB)- and cord blood (CB)-derived colony-forming unit-erythroids (CFU-Es) were treated in the absence or presence of dexamethasone (100 nM) for 24 hours. These cells were then processed for proteomics analysis by liquid chromatography–tandem mass spectrometry (LC-MS/MS). Proteomics quantified 10,045 proteins in PB samples and 10,028 proteins in CB samples....
- Subject
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AnemiaChronic DiseaseDrug Resistance
- Access Rights
- Free to All
- Local Expert
- Adrianna VlachosJeffrey LiptonLionel Blanc
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The Immune Cell Landscape in Kidneys of Lupus Nephritis Patients
Internal Dataset- Authors
- Arnon AraziDeepak A. RaoCeline BerthierAnne Davidson39 more author(s)...
- Description
Lupus nephritis is a potentially fatal autoimmune disease for which the current treatment is ineffective and often toxic. To develop mechanistic hypotheses of disease, we analyzed kidney samples from patients with lupus nephritis and from healthy control subjects using single-cell RNA sequencing. Our analysis revealed 21 subsets of leukocytes active in disease, including multiple populations of myeloid...
- Subject
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KidneyLupus NephritisRNA-SeqSequence Analysis, RNA
- Access Rights
- Free to all with registrationApplication Required
- Local Expert
- Anne DavidsonArnon AraziBetty Diamond
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Proteomic and single-cell transcriptomic dissection of human plasmacytoid dendritic cell response to influenza virus
Internal Dataset- Authors
- Mustafa GhanemAndrew ShihHouman KhaliliEmily Werth4 more author(s)...
- Description
Plasmacytoid dendritic cells (pDCs) represent a rare innate immune subset uniquely endowed with the capacity to produce substantial amounts of type-I interferons (IFN-I). This function of pDCs is critical for effective antiviral defenses and has been implicated in autoimmunity. While IFN-I and select cytokines have been recognized as pDC secreted products, a comprehensive agnostic profiling of the...
- Subject
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Influenza A Virus, H1N1 SubtypeInterferon Type IProteomicsRNA-Seq
- Access Rights
- Free to All
- Local Expert
- Andrew ShihPeter Gregersen
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Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci
Internal Dataset- Authors
- Maria Gutierrez-ArcelusYuriy BaglaenkoJatin AroraSusan Hannes14 more author(s)...
- Description
In this study we sought to analyze the effects of genetic variants on gene regulation in a cell-state dependent manner during CD4 memory T cell activation. To do this, we performed an RNA-seq time series experiment on CD4 memory T cells activated with anti-CD3/CD28 beads in individuals with no autoimmune disease. We measured gene expression levels, and allele-specific expression at heterozygous sites...
- Subject
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AutoimmunityGenetic VariationHLA AntigensHLA-DQ beta-ChainsLymphocyte ActivationPromoter Regions, GeneticRNA-Seq
- Access Rights
- Free to AllFree to all with registrationApplication Required
- Local Expert
- Peter Gregersen
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Next-Generation Standard RNA-Sequencing Analysis of human monocytes stimulated by HMGB1 with or without DMOG
Internal Dataset- Authors
- Travis PengShin-Yi DuMyoungsun SonBetty Diamond
- Description
We report the application of standard RNA-sequencing technology for high-throughput profiling of differential gene expression in mammalian cells. This study aims to compare differential gene expression in human monocytes in the absence or presence of HMGB1 and DMOG exposure would mimic hypoxia. Human monocytes (five million cells) from a healthy donor were divided into four groups in triplicate (control,...
- Subject
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Cell HypoxiaCOVID-19Hypoxia-Inducible Factor 1, alpha SubunitMonocytes
- Access Rights
- Free to All
- Local Expert
- Betty DiamondMyoungsun Son
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Developmental differences between neonatal and adult human erythropoiesis.
Internal Dataset- Authors
- Hongxia YanJohn HaleJulie JaffrayJie Li10 more author(s)...
- Description
RNA was extracted from FACS-sorted cells at 8 distinct stages of erythropoiesis, derived from CB- and PB-CD34+ cells. cDNA libraries were prepared using the Illumina TruSeq kit and sequenced on the Illumina HiSeq 2500 (Epigenomics Core of Weill Cornell Medical College, New York). This sequencing strategy produced ~15-80 million 50bp single end reads per sample. For each distinct stage of erythropoiesis,...
- Subject
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AgingErythropoiesisRNA-SeqTranscriptome
- Access Rights
- Free to All
- Local Expert
- Lionel Blanc
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NBQX disodium salt, an AMPA receptor antagonist, is used for an in vitro treatment of human smooth muscle cells
Internal Dataset- Authors
- Alessandro GallinaUrszula RykaczewskaRobert WirkaApril Caravaca12 more author(s)...
- Description
Vascular smooth muscle cells (VSMCs) are key constituents of both normal arteries and atherosclerotic plaques. They have an ability to adapt to changes in the local environment by undergoing phenotypic modulation. The amino-acid glutamate has been associated with CVD risk and VSMCs metabolism in experimental vascular research, and glutamate receptors regulate VSMC biology and promote pulmonary vascular...
- Subject
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GlutamatesMyocytes, Smooth MuscleRNA-SeqSequence Analysis, RNA
- Access Rights
- Free to All
- Local Expert
- Peder Olofsson
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Mortality in association with antipsychotic medication use and clinical outcomes among geriatric psychiatry outpatients with COVID-19
Internal Dataset- Authors
- Bienvenida AustriaRehana HaqueSukriti MittalJamie Scott5 more author(s)...
- Description
Includes both deidentified individual patient data and analysis outputs. Study included 56 patients. Demographic and clinical data including medication, diagnosis and Clinical Global Impression Severity (CGI-S) scales on outpatients who had COVID-19 between February 28th and October 1st 2020 were extracted from the electronic health records (EHR) from the hospital. Study observed a higher COVID-19...
- Subject
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Antipsychotic AgentsCOVID-19Mental DisordersOutpatients
- Access Rights
- Free to All
- Local Expert
- Bienvenida AustriaYun Freudenberg-Hua
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Quality improvement evaluation of a web-based continuing education program in blood pressure measurement
Internal Dataset- Authors
- Lauren BlockSarah FlynnLisa CooperCaroline Lentz3 more author(s)...
- Description
These datasets were compiled during a study to evaluate if a web-based continuing education program in blood pressure measurement reinforced knowledge and skills among clinical staff and promoted sustainability of an existing quality improvement program. Knowledge and skills of participating clinical staff were evaluated before and after viewing the continuing education module. The datasets consist...
- Subject
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Blood PressureEducation, Distance
- Access Rights
- Free to AllAuthor approval required
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DepMap
- Alternate Title(s)
- Cancer Dependency Map
- Description
The mutations that cause cancer cells to grow also confer specific vulnerabilities that normal cells lack. Some of these acquired alterations represent compelling therapeutic targets. The challenge is that, for the overwhelming majority of cancers, we do not fully understand the relationship between the genetic alterations of cancer and the dependencies they cause. To solve this problem, we are creating...
- Subject
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Big DataCancerGenomicsPrecision MedicineProteomics
- Access Rights
- Free to AllFree to all with registration
- Local Expert
- Nyasha Chambwe
Filter by
Subject Domain
- Cancer 9
- Genomics 9
- RNA-Seq 9
- Big Data 5
- COVID-19 5
- Sequence Analysis, RNA 4
- Genetic Variation 3
- Genome, Human 3
- Precision Medicine 3
- Autoimmunity 2
- Cohort Studies 2
- Electronic Health Records 2
- Genetic Predisposition to Disease 2
- HLA Antigens 2
- Inflammation 2
- Kidney 2
- Lupus Erythematosus, Systemic 2
- Monocytes 2
- Proteomics 2
- Retrospective Studies 2
- Stroke 2
- Aging 1
- Alleles 1
- Anemia 1
- Antipsychotic Agents 1
- Blood Pressure 1
- Breast Cancer 1
- Carcinoma, Ovarian Epithelial 1
- Cell Hypoxia 1
- Chromosome Mapping 1
- Chronic Disease 1
- Clinical Trial 1
- Cyclooxygenase 2 1
- Dendritic Cells 1
- Diabetes Mellitus, Type 1 1
- Drug Resistance 1
- Education, Distance 1
- Endometriosis 1
- Erythropoiesis 1
- Glutamates 1
- HLA-DQ beta-Chains 1
- Human Papillomavirus Viruses 1
- Hyperkalemia 1
- Hypoxia-Inducible Factor 1, alpha Subunit 1
- Infertility 1
- Influenza A Virus, H1N1 Subtype 1
- Interferon Regulatory Factors 1
- Interferon Type I 1
- Lupus Nephritis 1
- Lymphocyte Activation 1
- Membrane Proteins 1
- Mental Disorders 1
- MicroRNAs 1
- Myocytes, Smooth Muscle 1
- Neurology 1
- Neuromyelitis Optica 1
- Oropharyngeal Neoplasms 1
- Outpatients 1
- Ovarian Neoplasms 1
- Papilloma 1
- Polymerase Chain Reaction 1
- Promoter Regions, Genetic 1
- Single-Cell Analysis 1
- Social Determinants of Health 1
- Social Sciences 1
- Spinal Cord Injuries 1
- Tertiary Care Centers 1
- Transcriptome 1
- mice 1