DR7 DataRelease

SDY21: Gene Expression Study of TLR Responses on Dendritic Cells
Status: New
Description: Cytokine and gene expression profile after TLR activation of dendritic cells.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3YUM4W1N9
Subjects: 4
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke Human Vaccine Institute Duke Human Vaccine Institute
Publications:None
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 150
Luminex xMAP 5612
Clinical Assessments:None
SDY29: Determine of anti-PA titer kinetics
Status: New
Description: Four groups of 12 mice will each be immunized with rPA ± Alum (alhydrogel). Two groups will then be boosted on Day 227 with rPA alone. Mice will be bled every 2-3 days over the course of 283 days. Serum samples will be prepared and assayed for anti-PA titers using ELISA and/or anthrax toxin neutralization assays.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3VDXBDPRQ
Subjects: 48
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke Human Vaccine Institute Duke Human Vaccine Institute
Publications:None
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 4192
Clinical Assessments:None
SDY30: Comprehensive study of germinal center development and antibody response
Status: New
Description: To comprehensively study the humoral response to immunization with rPA with or without Alum using in vitro antibody analyses and tissue staining.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3THUFGISM
Subjects: 54
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke Human Vaccine Institute Duke Human Vaccine Institute
Publications:None
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 180
Flow Cytometry 445
Clinical Assessments:None
SDY31: Determining the effect of different adjuvants and doses on the immune response
Status: New
Description: Inbred C57BL/6 female mice (8-10 weeks old) were immunized subcutaneously according to the 8 immunization groups. Serum samples were collected weekly from 2 staggered groups and analyzed for PA-specific (Total Ig, IgG1, IgG2a, and IgG3) and neutralizing antibody titers. Also, spleen, thymus, and brachial and inguinal lymph nodes will be harvested from 1 of each group at 4 time points for histology.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M37IXT07LU
Subjects: 96
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke Human Vaccine Institute Duke Human Vaccine Institute
Publications:None
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 1788
Flow Cytometry 617
Clinical Assessments:None
SDY32: Determining the effect of different adjuvants and doses on the immune response to rPA
Status: New
Description: Inbred C57BL/6 female mice (12-15 weeks old) were immunized subcutaneously according to the 7 immunization groups. Serum samples were collected weekly from subgroup A and analyzed serum antibody response using ELISA, Toxin Neutralization Assays, and Surface Plasmon Resonance. Also, brachial and inguinal lymph nodes were harvested from 3 of each group at 10 time points. Lymph nodes from one side of each mouse were used for histology and nodes from the other side were used for phenotyping by flow cytometry.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3OL4ZG9JN
Subjects: 210
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke Human Vaccine Institute Duke Human Vaccine Institute
Publications:None
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 2290
Flow Cytometry 8309
Clinical Assessments:None
SDY224: Immune Responses to Seasonal TIV 2010-2011 Influenza Vaccination in Humans (see companion study SDY396,SDY564)
Status: New
Description: High-frequency sampling combined with systems biology analysis of human peripheral blood cells following influenza vaccination was used to investigate T cell and B cell responses. Functional principal component analysis was used to examine time varying B cell vaccine response highlighting a single subject-specific mathematical pattern explaining ninety percent of the transcriptome variation. In addtition, daily sampling and monitoring of the proliferation marker Ki-67, revealed influenza-specific CD4 T cells do respond to vaccination.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense II University of Rochester Center for Biodefense Immune Modeling II
DOI: 10.21430/M37KMO7JLW
Subjects: 14
Study PI, contact:
NameOrganizationSite
Hulin Wu University of Rochester Medical Center University of Rochester Medical Center
Martin Zand University of Rochester Medical Center University of Rochester Medical Center
Publications:
Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.. Vaccine. Jun 2012. doi: 10.1016/j.vaccine.2012.04.059. Epub 2012 Apr 30. [Pubmed: 22554464]
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.. Sci Rep. - 2013. doi: 10.1038/srep02327. [Pubmed: 23900141]
Resources:
University of Rochester Center for Biodefense Immune Modeling https://cbim.urmc.rochester.edu/]
Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/sra?term=SRX259436]
Effect of influenza vaccination on PBMC and B cell gene expression profiles in healthy humans http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE45764]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 423
ELISPOT 120
Flow Cytometry 560
Hemagglutination Inhibition 543
Q-PCR 1548
Sequencing 110
Clinical Assessments:None
SDY256: Cooperation between DCs and basophils in TH2 response to papain
Status: New
Description: To investigate the contribution of dendritic cells and basophils to TH2 differentiation, induction with OVA and papain was used to investigate signalling in both in vivo and in vitro systems.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3GCSV0KAE
Subjects: 211
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke University Emory University
Publications:
The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.. Nat Immunol. Jul 2010. doi: 10.1038/ni.1883. Epub 2010 May 23. [Pubmed: 20495560]
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 211
Clinical Assessments:None
SDY258: Dendritic cells and TH2 differentiation in vivo
Status: New
Description: TH2 cell differentiation was investigated by measuring IL-4 output after OVA plus papain challenge in normal and dendritic-cell depleted mice. The role of migrating dermal dendritic cells in OVA plus papain challenge by blocking migration and depleting dendritic cell subtypes.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3F0JEOKSX
Subjects: 281
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke University Emory University
Publications:
The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.. Nat Immunol. Jul 2010. doi: 10.1038/ni.1883. Epub 2010 May 23. [Pubmed: 20495560]
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 281
Clinical Assessments:None
SDY259: Reactive oxygen species and TH2 responses to papain
Status: New
Description: The role of reactive oxygen species in the TH2 response to papain was investigated. The production of ROS by dendritic cells both in vivo and in vitro was examined as an inducer of TH2 differentiation and suppressor of TH1 differentiation. CD70 and IL-12 as effectors of ROS-mediated suppression of TH1 differentiation were investigated as well as the effect of ROS on IL-4-mediated TH2 response.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3DWBGXETN
Subjects: 212
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke University Emory University
Publications:
The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.. Nat Immunol. Jul 2010. doi: 10.1038/ni.1883. Epub 2010 May 23. [Pubmed: 20495560]
Resources:
Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21602]
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 8
Flow Cytometry 204
Clinical Assessments:None
SDY260: The role of TLR4 and TRIF signaling in TH2 response to papain
Status: New
Description: The role of TLR4 signalling in TH2 response to papain was measured by IL-4 and antibody production. The involvement of MyD88, TRIF, and oxidized phospholipids in the TLR4 pathway was examined. Basophil recruitment to the draining lymph node through dendritic-cell-secreted CCL7 was investigated as a component of the TLR4/TRIF pathway.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense Multiscale Systems Immunology for Adjuvant Development
DOI: 10.21430/M3KIQA4LOV
Subjects: 110
Study PI, contact:
NameOrganizationSite
Thomas Kepler Duke University Emory University
Publications:
The T helper type 2 response to cysteine proteases requires dendritic cell-basophil cooperation via ROS-mediated signaling.. Nat Immunol. Jul 2010. doi: 10.1038/ni.1883. Epub 2010 May 23. [Pubmed: 20495560]
Resources:
Center for Computational Immunology http://www.bu.edu/computationalimmunology/]
Assays:
Assay TypeNumber of Exp. Samples
Flow Cytometry 110
Clinical Assessments:None
SDY180: Systems scale interactive exploration reveals quantitative and qualitative differences in response to 2009-2010 Fluzone influenza vaccine and pneumococcal vaccine
Status: Updated
Description: Systems immunology approaches were employed to investigate innate and adaptive immune responses to influenza and pneumococcal vaccines. These two non-live vaccines show different magnitudes of transcriptional responses at different time points af- ter vaccination. Software solutions were developed to explore correlates of vaccine efficacy measured as antibody titers at day 28. These enabled a further dissection of transcriptional responses. Thus, the innate response, measured within hours in the peripheral blood, was dominated by an interferon transcriptional signature after influenza vaccination and by an inflammation signature after pneumo- coccal vaccination. Day 7 plasmablast responses induced by both vaccines was more pronounced after pneumococcal vaccination. Together, these results suggest that comparing global immune responses elicited by different vaccines will be critical to our understanding of the immune mechanisms underpinning successful vaccination.
Program/Contract:
ProgramContract
Human Immunology Project Consortium 1 (HIPC1) Systems Analysis Vaccine Responses in Healthy and Hyporesponsive Humans
DOI: 10.21430/M3I44H8R17
Subjects: 46
Study PI, contact:
NameOrganizationSite
A. Karolina Palucka Baylor Reasearch Institute Baylor Reasearch Institute
Publications:
Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines.. Immunity. Apr 2013. doi: 10.1016/j.immuni.2012.12.008. [Pubmed: 23601689]
Resources:
Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE30101]
Assays:
Assay TypeNumber of Exp. Samples
DNA microarray 542
Flow Cytometry 2208
Hemagglutination Inhibition 66
Luminex xMAP 229
Nanostring 18
Transcription profiling by array 161
Virus Neutralization 89
Clinical Assessments:None
SDY241: Simulation and Prediction of the Adaptive Immune Response and Quantification of Early and Adaptive Immune Response Kinetics to Influenza A Virus Infection
Status: Updated
Description: Seasonal and pandemic influenza A virus (IAV) continues to be a public health threat. Modeling approaches were used combined with experimental data to investigate innate and adaptive immune responses to IAV infection. Mathematical models developed describe the dynamic interactions between influenza virus, target cells, cytotoxic lymphocytes, and virus-specific IgG and IgM. A two-compartment model developed quantifies the effects of viral replication and adaptive immunity.
Program/Contract:
ProgramContract
Modeling Immunity for Biodefense University of Rochester Center for Biodefense Immune Modeling
DOI: 10.21430/M3ERWHDJEO
Subjects: 494
Study PI, contact:
NameOrganizationSite
David Topham University of Rochester University of Rochester
Hulin Wu University of Rochester University of Rochester
Publications:
Simulation and prediction of the adaptive immune response to influenza A virus infection.. J Virol. Jul 2009. doi: 10.1128/JVI.00098-09. Epub 2009 May 13. [Pubmed: 19439465]
Quantifying the early immune response and adaptive immune response kinetics in mice infected with influenza A virus.. J Virol. Jul 2010. doi: 10.1128/JVI.00266-10. Epub 2010 Apr 21. [Pubmed: 20410284]
Modeling of influenza-specific CD8+ T cells during the primary response indicates that the spleen is a major source of effectors.. J Immunol. Nov 2011. doi: 10.4049/jimmunol.1101443. Epub 2011 Sep 23. [Pubmed: 21948988]
Functionally Distinct Subpopulations of CpG-Activated Memory B Cells.. Sci Rep. - 2012. doi: 10.1038/srep00345. Epub 2012 Mar 30. [Pubmed: 22468229]
Ki-67 expression reveals strong, transient influenza specific CD4 T cell responses after adult vaccination.. Vaccine. Jun 2012. doi: 10.1016/j.vaccine.2012.04.059. Epub 2012 Apr 30. [Pubmed: 22554464]
High-resolution temporal response patterns to influenza vaccine reveal a distinct human plasma cell gene signature.. Sci Rep. - 2013. doi: 10.1038/srep02327. [Pubmed: 23900141]
Resources:
University of Rochester Center for Biodefense Immune Modeling https://cbim.urmc.rochester.edu/]
Immune Epitope Database (IEDB) http://www.iedb.org/reference/1024464]
Assays:
Assay TypeNumber of Exp. Samples
ELISA 1866
ELISPOT 485
Flow Cytometry 5090
Clinical Assessments:None
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