About
This project houses all the publicly available datasets generated by the Hi-IMPAcTB consortium over the course of its 7+ years.
What is Hi-IMPAcTB?
Hi-IMPAcTB is an ambitious endeavor bringing together a team of international, interdisciplinary researchers to improve our understanding of host-pathogen interactions in the context of tuberculosis (TB). Funded by a multi-center contract from the NIH, the long-term goal of the consortium is to enable principled vaccine design by improving our understanding of the protective versus non-protective immunological host response to infection with TB’s causal agent the bacterium Mycobacterium tuberculosis (Mtb). Hi-IMPAcTB is one of three centers receiving funding from NIAID to enable this vision. See here for more details.
The Data.
Using multi-modal data from lungs and blood in mice, non-human primates (NHPs) and humans the consortium aims to understand the range of immunological responses observed in each species and their association with TB disease outcome.
This involves the characterization of various components of the immune system and the interactions between them using (1) multi-parameter flow cytometery/CyToF and (2) single cell sequencing (including TCR sequencing) to understand changes in cellular composition and state after infection with Mtb. That is complemented by (3) systems serology data which allows profiling the humoral immune response which recent evidence suggests might play an overlooked role in the Mtb response, as well as (4) a range of innate immune profiling assays which allow the characterization of macrophages, neutrophils and other non-adaptive immune cell types that play a role in determining disease outcome. (5) PET-CT imaging allows tracking disease development in live animals and in humans, and (6) Immunohistochemistry/fluorescence and (7) spatial transcriptomics allow the spatial profiling of tissues of interest. (8) Using a genetically barcoded clinical strain of Mtb, we can also trace the establishment of persistent TB lesions and determine bacterial dissemination from the lung (the original site of exposure) to other tissues of interest such as lymphnodes.
A notable advantage is the consortium’s ability to use a range of interventions in NHPs and genetically diverse mouse strains to untangle correlation/association from causation in the context of immune protection against disease. This is especially important given that most common laboratory mouse strains do not closely recapitulate the disease response seen in humans. Another is that we profile patients with a range of clinical presentations of TB disease, reflecting a more nuanced appreciation for a spectrum of disease states.
Whenever possible, data is deposited in an appropriate public repository and linked here with all relevant metadata to enable FAIR sharing.
The role of Data Science.
Given the complexity of the data, clinicians, experimental biologists, and computational biologists within the consortium work closely to integrate and analyze the data to inform our understanding of the complex host response to Mtb in association with clinically-relevant outcomes. This involves the adoption of existing statistical and mathematical frameworks, and the development of new tools adapted to handling the specific design of animal and clinical studies in the consortium. Emerging hypotheses can then be tested in vivo, and the new data subsequently used to refine model performance in a virtuous cycle that we hope will enable the identification of clinically-relevant vaccination strategies.
All the original code used to analyze any of our data is publicly deposited and linked to on FAIRDOMHUB in the context in which it was used.
The Team.
The data and code in this project primarily comes from the following Hi-IMPAcTB laboratories:
- Fortune Lab (co-lead PI), Harvard University, USA.
- Flynn Lab (co-lead PI), University of Pittsburgh, USA.
- Boom Lab (co-lead PI), Case Western Reserve University, USA*
- Mayanja-Kizza Lab, Makerere University, Uganda*
- Bryson Lab, MIT, USA.
- Lauffenburger Lab, MIT, USA
- Shalek Lab, MIT, USA.
- BioMicro Center, MIT, USA
- Systems Serology Lab, Ragon Institute, USA
- Behar Lab, University of Massachussets Worcester, USA
- Sassetti Lab, University of Massachusets Worcester, USA
- Seshadri Lab, University of Washington, USA
- Nemes Lab, University of Cape Town/SATVI, South Africa
- Waltzl Lab, Stellenbosch University, South Africa
- Wong Lab, AHRI, South Africa
*Participants in the Uganda-CWRU partnership.
Programme: NExtSEEK
SEEK ID: https://fairdomhub.org/projects/222
Funding codes:- 75N93019C00071-0-9999-1
Public web page: https://grantome.com/grant/NIH/75N93019C00071-0-9999-1
Organisms: Mus musculus, Homo sapiens, Macaca fascicularis, Macaca mulatta
FAIRDOM PALs: No PALs for this Project
Project created: 13th Jan 2021

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- People (8)
- Programmes (1)
- Institutions (3)
- Investigations (1)
- Studies (16+1)
- Assays (165)
- Data files (237+12)
- SOPs (97+5)
- Sample types (129+103)
- Samples (28387+1620)
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Institutions: Massachusetts Institute of Technology
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Institutions: MIT, Massachusetts Institute of Technology
Projects: Hi-IMPAcTB
Institutions: Massachusetts Institute of Technology

Projects: Hi-IMPAcTB, MIT SRP
Institutions: Massachusetts Institute of Technology
Researcher at BioMIcro Center, Data Management and Analysis Core; Massachusetts Institute of Technology
Projects: Hi-IMPAcTB, MIT SRP
Institutions: Massachusetts Institute of Technology
Projects: Hi-IMPAcTB
Institutions: University of Toronto
Projects: MIT SRP, Hi-IMPAcTB, MetNet, Endometriosis, Cancer Systems Biology Consortium (CSBC), Shoulders Lab
Web page: https://nextseek.mit.edu/
Submitter: Dikshant Pradhan
Studies: Age and sex influence antibody profiles associated with tuberculosis pro..., Antibody-Fab and -Fc features promote Mycobacterium tuberculosis restric..., CD4+ T cells re-wire granuloma cellularity and regulatory networks to pr..., CD8+ lymphocytes are critical for early control of tuberculosis in macaques, Comparable Non-canonical T cell responses are associated with protection..., Fc-engineered antibodies leverage neutrophils to drive control of Mycoba..., High-dose intravenous BCG vaccination induces enhanced immune signaling ..., Humoral correlates of protection against Mycobacterium tuberculosis foll..., Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resis..., Intravenous BCG-mediated protection against tuberculosis requires CD4+ T..., Multi-modal data integration using Markov Field graphical networks predi..., Multimodal profiling of lung granulomas in macaques reveals cellular cor..., Robust IgM responses following intravenous vaccination with Bacille Calm..., Specific CD4+ T cell phenotypes associate with bacterial control in peop..., Systematic deconstruction of myeloid cell signaling in tuberculosis gran..., Systems-level computational translation of mouse and human transcriptomi...
Assays: ADCD Analysis - Data Linked, ADFP Analysis - Data Linked, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, All Metadata, Anti-Microbial Assay – Metadata, Antibody Challenge - Metadata, Antibody Dependent Complement Deposition - Data Linked, Antibody Dependent Functional Profiling - Data Linked, Antibody Titer - Data Linked, Antibody Titer Analysis - Data Linked, Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis Analysis - Data Linked, Antibody-Dependent NK Cell Activation - Data Linked, Antibody-Dependent NK Cell Activation Analysis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis Analysis - Data Linked, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Extraction - Metadata, Bacterial Survivability Restriction Assay - Data Linked, Bacterial Survivability Restriction Assay - Data Linked, Bacterial Survivability Restriction Assay: Validation Data - Data Attached, CITESEQ Analysis - Data Linked, Cell Extraction - Metadata, Cell Extraction: Validation Data - Metadata, Cell Isolation - Metadata, Cell Isolation - Metadata, Cell Sorting – Data Linked, DNA Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Digitally Barcoded Mtb Matrix Analysis - Data Attached, ELISA - Data Linked, ELISA Assay - Data Linked, FC Receptor Binding - Data Linked, FC Receptor Binding Analysis - Data Linked, FC Receptor Binding Assay - Data Linked, FC-Receptor Binding Assay - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Attached, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Analysis - Data Linked, Flow Cytometry Processing – Data Attached, Flow Cytometry – Data Linked, Functional Assay – Metadata, Gene Expression Analysis - Data Linked, Gene Expression Analysis: Training Data - Data Linked, Gene Expression Analysis: Validation Data - Data Linked, Glycosylation Assay - Data Linked, Histology - Data Linked, Immunohistochemistry - Data Linked, Immunohistochemistry - Data Linked, Immunohistochemistry – Data Linked, Library Creation - Metadata, Library Creation - Metadata, Library Creation - Metadata, Library Creation – Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep - Metadata, Library Prep: Training Data - Metadata, Library Prep: Validation Data - Metadata, Linear Mixed Model - Data Linked, Luminex - Data Linked, Luminex Assay – Metadata, Luminex Data Processing – Data Attached, Mass Cytometry - Data Linked, Mass Cytometry Analysis - Data Linked, Model Validation, Model Validation - Data Linked, Mouse Challenge – Metadata, NHP Necropsy – Metadata, NHP Tissue Collection – Metadata, PCR: Validation Data - Data Attached, PET-CT Scan - Data Linked, PET-CT Scan - Data Linked, PET-CT Scan Analysis – Data Linked, PET-CT Scan – Data Linked, PET/CT Scan - Data Linked, PET/CT Scan - Data Linked, Pathogen Challenge and Antibody Depletion - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit - Metadata, Patient Visit – Metadata, Patient Visit – Metadata, RNA Extraction: Validation Data - Metadata, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing - Data Linked, Short Read Sequencing: Training Data - Data Linked, Short Read Sequencing: Validation Data - Data Linked, Single Cell Clustering - Data Linked, Single Cell Clustering Analysis - Data Linked, Single Cell Clustering Analysis – Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Single Cell Expression Matrix Analysis – Data Linked, Single Cell Sequencing – Data Linked, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection - Metadata, Tissue Collection – Metadata, Tissue Collection: Training Data - Metadata, Tissue Extraction - Metadata, Titer Assay - Data Linked, Titer Assay - Data Linked, Titer Assay Analysis - Data Linked, TransCompR Cross Species Modeling - Data Linked, Western Blot - Data Linked
Snapshots: No snapshots
Patricia S. Grace, Joshua M. Peters, Jaimie Sixsmith, Richard Lu, Corinne Luedeman, Brooke A. Fenderson, Andrew Vickers, Matthew D. Slein, Edward B. Irvine, Tanya McKitrick, Mo-Hui Wei, Richard D. Cummings, Aaron Wallace, Lisa A. Cavacini, Alok Choudhary, Megan K. Proulx, Christopher Sundling, Gunilla Källenius, Rajko Reljic, Joel D. Ernst, Arturo Casadevall, Camille Locht, Abraham Pinter, Christopher M. Sasseti, Bryan D. Bryson, Sarah M. Fortune, Galit Alter
...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: ADCD Analysis - Data Linked, ADFP Analysis - Data Linked, All Metadata, Antibody Dependent Complement Deposition - Data Linked, Antibody Dependent Functional Profiling - Data Linked, Bacterial Survivability Restriction Assay - Data Linked, Cell Extraction - Metadata, Cell Sorting – Data Linked, ELISA Assay - Data Linked, FC-Receptor Binding Assay - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Mouse Challenge – Metadata, Short Read Sequencing - Data Linked, Single Cell Clustering - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection – Metadata, Western Blot - Data Linked
Snapshots: No snapshots
Joshua M. Peters, Hannah P. Gideon, Travis K. Hughes, Cal Gunnarson, Pauline Maiello, Douaa Mugahid, Sarah K. Nyquist, Joshua D. Bromley, Paul C. Blainey, Beth F. Junecko, Molly L. Nelson, Douglas A. Lauffenburger, Philana Ling Lin, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Joshua T. Mattila, Bryan D. Bryson
DOI: https://www.biorxiv.org/content/10.1101/2024.05.24.595747v1.full
Additional Datasets:
- More Metadata associated with these NHPs exists ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Cell Isolation - Metadata, Gene Expression Analysis - Data Linked, Immunohistochemistry - Data Linked, Library Creation - Metadata, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Snapshots: No snapshots
Megan K. Proulx, Christine D. Wiggins, Charlotte J. Reames, Claire Wu, Michael C. Kiritsy, Patricia Grace, Clare M. Smith, Cecelia S. Lindestam Arlehamn, Galit Alter, Douglas A. Lauffenburger, Christopher M. Sassetti
Training Data for the Model: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE267774
Abstract: While control of Mycobacterium tuberculosis (Mtb) infection is generally understood to require a Th1-immune response and IFN secretion, infection ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: CITESEQ Analysis - Data Linked, Cell Isolation - Metadata, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Histology - Data Linked, Library Prep - Metadata, Model Validation - Data Linked, Pathogen Challenge and Antibody Depletion - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Snapshots: No snapshots
Krista M. Pullen, Ryan Finethy, Seung-Hyun B. Ko, Charlotte J. Reames, Christopher M. Sassetti, Douglas A. Lauffenburger
DOI:
Abstract:Numerous studies have identified similarities in blood transcriptomic signatures of mouse tuberculosis (TB) models and human disease phenotypes, such as type 1 interferon (IFN) production and innate immune cell activation, yet the pathophysiology observed in murine infection does not recapitulate some of the hallmarks of human ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Survivability Restriction Assay: Validation Data - Data Attached, Cell Extraction: Validation Data - Metadata, Gene Expression Analysis: Training Data - Data Linked, Gene Expression Analysis: Validation Data - Data Linked, Library Prep: Training Data - Metadata, Library Prep: Validation Data - Metadata, PCR: Validation Data - Data Attached, RNA Extraction: Validation Data - Metadata, Short Read Sequencing: Training Data - Data Linked, Short Read Sequencing: Validation Data - Data Linked, Tissue Collection: Training Data - Metadata, TransCompR Cross Species Modeling - Data Linked
Snapshots: No snapshots
_Andrew W. Simonson, Joseph J. Zeppa, Allison N. Bucsan, Michael C. Chao, Supriya Pokkali, Forrest Hopkins, Michael R. Chase, Andrew J. Vickers, Matthew S. Sutton, Caylin G. Winchell, Amy J. Myers, Cassaundra L. Ameel, Ryan Kelly, Ben Krouse, Luke E. Hood, Jiaxiang Li, Chelsea C. Lehman, Megha Kamath, Jaime Tomko, Mark A. Rodgers, Rachel Donlan, Harris Chishti, H. Jacob Borish, Edwin Klein, Charles A. Scanga, Sarah Fortune, Philana Ling Lin, Pauline Maiello, Mario Roederer, Patricia A. Darrah, ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Bacterial Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Library Prep - Metadata, PET-CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Tissue Collection - Metadata
Snapshots: No snapshots
Joshua M. Peters, Edward B. Irvine, Jacob M. Rosenberg, Marc H. Wadsworth II, Travis K. Hughes, Matthew Sutton, Sarah K. Nyquist, Joshua D. Bromley, Rajib Mondal, Mario Roederer, Robert A. Seder, Patricia A. Darrah, Galit Alter, JoAnne L. Flynn, Alex K. Shalek, Sarah M. Fortune, Bryan D. Bryson
DOI: https://www.science.org/doi/10.1126/sciadv.adq8229
Intradermal Bacillus Calmette-Guérin (BCG) is the most widely administered vaccine, but it does not sufficiently ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Library Creation - Metadata, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Snapshots: No snapshots
Leela RL Davies, Chuangqi Wang, Pia Steigler, Kathryn A Bowman, Stephanie Fischinger, Mark Hatherill, Michelle Fisher, Staney Kimbung Mbandi, Miguel Rodo, Tom HM Ottenhoff, Hazel M Dockrell, Jayne S Sutherland, Harriet Mayanja-Kizza, W Henry Boom, Gerhard Walzl, Stefan H.E. Kaufmann, Elisa Nemes, Thomas J Scriba, Douglas Lauffenburger, Galit Alter, Sarah M. Fortune.
Link to Paper: https://doi.org/10.1038/s41564-024-01678-x
Abstract: Antibody features vary ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, FC Receptor Binding Assay - Data Linked, Linear Mixed Model - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata, Titer Assay - Data Linked
Snapshots: Snapshot 1
Joshua D. Bromley, Sharie Keanne C. Ganchua, Sarah K. Nyquist, Pauline Maiello, Michael Chao, H. Jacob Borish, Mark Rodgers, Jaime Tomko, Kara Kracinovsky, Douaa Mugahid, Son Nguyen, Dennis Wang, Jacob M. Rosenberg, Edwin C. Klein, Hannah P. Gideon, Roisin Floyd-O’Sullivan, Bonnie Berger, Charles A Scanga, Philana Ling Lin, Sarah M. Fortune, Alex K. Shalek, JoAnne L. Flynn
Link to Paper: https://www.cell.com/immunity/fulltext/S1074-7613(24)00375-3
Immunological ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Library Prep - Metadata, PET-CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Snapshots: No snapshots
Shu Wang, Amy J Myers, Edward B Irvine, Chuangqi Wang, Pauline Maiello, Mark A Rodgers, Jaime Tomko, Kara Kracinovsky, H. Jacob Borish, Michael C Chao, Douaa Mugahid, Patricia A. Darrah, Robert A. Seder, Mario Roederer, Charles A Scanga, Philana Ling Lin, Galit Alter, Sarah M Fortune, JoAnne L Flynn, Douglas A Lauffenburger
Paper Link: https://doi.org/10.1101/2024.04.13.589359
Link to Model Validation Datasets: https://fairdomhub.org/studies/1198
Abstract: ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Antibody Titer - Data Linked, Antibody Titer Analysis - Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Model Validation, PET/CT Scan - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
Snapshots: No snapshots
Meng Sun*, Jolie M. Phan*, Nathan S. Kieswetter, Krystle K.Q. Yu, Malisa T. Smith, Huang Huang, Sanjana Gupta, Gerlinde Obermoser, Holden Terry Maecker, Akshaya Krishnan, Neha Gupta, Mary Rieck, Peter Acs, Mustafa Ghanizada, Shin-Heng Chiou, Purvesh Khatri, W. Henry Boom, Thomas R. Hawn, Catherine M. Stein, Harriet Mayanja-Kizza, Mark M. Davis*, Chetan Seshadri*
Abstract: A subset of individuals with a high probability of exposure to M. tuberculosis (M.tb) ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata
Snapshots: Snapshot 1
Caylin G. Winchell, Sarah K. Nyquist, Michael C. Chao, Pauline Maiello, Amy J. Myers, Forrest Hopkins, Michael Chase, Hannah P. Gideon, Kush V. Patel, Joshua D. Bromley, Andrew W. Simonson, Roisin Floyd-O’Sullivan, Marc Wadsworth, Jacob M. Rosenberg, Rockib Uddin, Travis Hughes, Ryan J. Kelly, Josephine Griffo, Jaime Tomko, Edwin Klein, Bonnie Berger, Charles A. Scanga, Joshua Mattila, Sarah M. Fortune, Alex K. Shalek, Philana Ling Lin, JoAnne L. Flynn; CD8+ lymphocytes are critical for early ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: All Metadata, Bacterial Extraction - Metadata, DNA Extraction - Metadata, Digitally Barcoded Mtb Matrix Analysis - Data Attached, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Attached, Immunohistochemistry - Data Linked, PET/CT Scan - Data Linked, Patient Visit - Metadata, Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Collection - Metadata
Snapshots: Snapshot 1, Snapshot 2
Edward B. Irvine, Joshua M. Peters, Richard Lu, Patricia S. Grace, Jaimie Sixsmith, Aaron Wallace, Matthew Schneider, Sally Shin, Wiktor Karpinski, Jeff C. Hsiao, Esther van Woudenbergh, Arturo Casadevall, Bryan D. Bryson, Lisa Cavacini, Galit Alter, Sarah M. Fortune doi: https://doi.org/10.1101/2022.05.01.490220
Novel vaccination and therapeutic strategies are urgently needed to mitigate the tuberculosis (TB) epidemic. While extensive efforts have focused ...
Submitter: Jake Schissel
Investigation: IMPAcTB
Assays: All Metadata, Antibody Challenge - Metadata, Antibody-dependent Cellular Phagocytosis - Data Linked, Antibody-dependent Complement Deposition - Data Linked, Antibody-dependent NK Cell Activation - Data Linked, Antibody-dependent Neutrophil Phagocytosis - Data Linked, Bacterial Challenge - Metadata, Bacterial Survivability Restriction Assay - Data Linked, ELISA - Data Linked, Glycosylation Assay - Data Linked, Library Prep - Metadata, Luminex - Data Linked, Patient Visit - Metadata, Single Cell Clustering Analysis - Data Linked, Single Cell Expression Analysis - Data Linked, Tissue Extraction - Metadata
Snapshots: No snapshots
Edward B Irvine, Patricia A Darrah, Shu Wang, Chuangqi Wang, Ryan P McNamara, Mario Roederer, Robert A Seder, Douglas A Lauffenburger, JoAnne L Flynn, Sarah M Fortune, Galit Alter
https://doi.org/10.1101/2023.07.31.551245
Altering the route of Bacille Calmette-Guérin (BCG) immunization from low-dose intradermal vaccination to high-dose intravenous (IV) vaccination resulted in a high level of protection against Mycobacterium tuberculosis ( Mtb ) infection, ...
Submitter: Charles Demurjian
Investigation: IMPAcTB
Assays: Antibody-Dependent Cellular Phagocytosis - Data Linked, Antibody-Dependent Cellular Phagocytosis Analysis - Data Linked, Antibody-Dependent NK Cell Activation - Data Linked, Antibody-Dependent NK Cell Activation Analysis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis - Data Linked, Antibody-Dependent Neutrophil Phagocytosis Analysis - Data Linked, FC Receptor Binding - Data Linked, FC Receptor Binding Analysis - Data Linked, Patient Visit - Metadata, Tissue Collection - Metadata, Titer Assay - Data Linked, Titer Assay Analysis - Data Linked
Snapshots: No snapshots
Hannah P.Gideon, Travis K.Hughes, Constantine N.Tzouanas, Marc H.WadsworthII, Ang AndyTu, Todd M.Gierahn, Joshua M.Peters, Forrest F.Hopkins, Jun-RongWei, Conner Kummerlowe, Nicole L.Grant, Kievershen Nargan, Jia YaoPhuah, H. JacobBorish, Pauline Maiello, Alexander G.White, Caylin G.Winchell, Sarah K.Nyquist, Sharie Keanne C.Ganchua, Amy Myers, Kush V.Patel, Cassaundra L.Ameel, Catherine T.Cochran, Samira Ibrahim, Jaime A.Tomko, Lonnie JamesFrye, Jacob ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Immunohistochemistry – Data Linked, Library Creation – Metadata, NHP Necropsy – Metadata, PET-CT Scan Analysis – Data Linked, PET-CT Scan – Data Linked, Patient Visit – Metadata, Single Cell Clustering Analysis – Data Linked, Single Cell Expression Matrix Analysis – Data Linked, Single Cell Sequencing – Data Linked
Snapshots: Snapshot 1
Thiel BA, Worodria W, Nalukwago S, Nsereko M, Sanyu I, Rejani L, Zawedde J, Canaday DH, Stein CM, Chervenak KA, Malone LL, Kiyemba R, Silver RF, Johnson JL, Mayanja-Kizza H, Boom WH. Immune cells in bronchoalveolar lavage fluid of Ugandan adults who resist versus those who develop latent Mycobacterium tuberculosis infection. PLoS One. 2021 Apr 9;16(4):e0249477. doi: 10.1371/journal.pone.0249477. PMID: 33836031; PMCID: PMC8034721.
Abstract: ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Flow Cytometry Processing – Data Attached, Flow Cytometry – Data Linked, Patient Visit – Metadata, Tissue Collection - Metadata
Snapshots: Snapshot 1, Snapshot 2
Development of an effective tuberculosis (TB) vaccine has suffered from an incomplete understanding of the correlates of protection against Mycobacterium tuberculosis (Mtb). Intravenous (i.v.) vaccination with Bacille Calmette–Guérin (BCG) provides nearly complete protection against TB in rhesus macaques, but the antibody response it elicits remains incompletely defined. Here we show that i.v. BCG drives superior antibody responses in the plasma and the lungs of rhesus macaques compared to ...
Submitter: Dikshant Pradhan
Investigation: IMPAcTB
Assays: Anti-Microbial Assay – Metadata, Functional Assay – Metadata, Luminex Assay – Metadata, Luminex Data Processing – Data Attached, NHP Tissue Collection – Metadata
Snapshots: Snapshot 1
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: No SOPs
Data files: CEX-samples-publish2022-01-28_00-10.xlsx, NHP-samples-publish2022-01-28_00-20.xlsx
Snapshots: No snapshots
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-211020-V1_NHP-FcR-Luminex-Protocol-EI.doc, P.ALT-211020-V1_NHP-Isotype-Luminex-Protocol-EI..., P.ALT-211203-V1_BCG_study_EI_luminex_panel.xlsx
Data files: D.LMX-211203ALT-10_FcR_luminex_FcyR3A_plasma.xlsx, D.LMX-211203ALT-1_isotype_luminex_IgG1_BAL.xlsx, D.LMX-211203ALT-2_isotype_luminex_IgA_BAL.xlsx, D.LMX-211203ALT-3_isotype_luminex_IgM_BAL.xlsx, D.LMX-211203ALT-4_isotype_luminex_IgG1_plasma.xlsx, D.LMX-211203ALT-5_isotype_luminex_IgA_plasma.xlsx, D.LMX-211203ALT-6_isotype_luminex_IgM_plasma.xlsx, D.LMX-211203ALT-7_FcR_luminex_FcyR2A_BAL.xlsx, D.LMX-211203ALT-8_FcR_luminex_FcyR3A_BAL.xlsx, D.LMX-211203ALT-9_FcR_luminex_FcyR2A_plasma.xlsx, D.LMX-samples-publish2022-01-27_23-57.xlsx
Snapshots: No snapshots
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-220127-V1_EI-IV_BCG_PLS-DA_Statistics.docx
Data files: A.LMX-samples-publish2022-01-27_23-59.xlsx, D.FILE-220127ALT-1_Data_EI_IV_BCG_IgM_SystemsSe..., D.FILE-samples-publish2022-01-28_00-04.xlsx
Snapshots: No snapshots
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-211119-V1_Mac-Live-Dead-Protocol-EI.docx, P.ALT-211119-V1_Mac-Lux-Opsonize-Protocol-EI.docx, P.ALT-211119-V1_Mac-Lux-Protocol-EI.docx
Data files: No Data files
Snapshots: No snapshots
Submitter: Dikshant Pradhan
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-211020-V1_LAM-ADCP-Protocol-EI.doc, P.ALT-211020-V1_LAM-ADNP-Protocol-EI.doc, P.ALT-211101-V1_LAM-ADNKA-Protocol-EI.doc
Data files: No Data files
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-220823-V1_P---Mtb-Infection.rtf, P.FLY-220823-V1_P---NHP_housing.docx, P.FLY-220823-V1_P---Necropsy.docx, P.FLY-220823-V1_P---PET_CT_Imaging.docx
Data files: NHP-samples-publish2022-09-28_17-30.xlsx, PAV-samples-publish2022-11-3_15-09.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-220823-V1_P---Bacteria-Burden.docx, P.FLY-220823-V1_P---Chromosomal-Equivalents.rtf, P.FLY-220823-V1_P---Necropsy.docx
Data files: PAV-samples-publish2022-11-3_15-09.xlsx, TIS-samples-publish2022-10-11_23-37.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-210708-V1_Hannah's-GentleMacs-Protocol-as..., P.SHA-220819-V1_SeqWellHughes.et.al.Master.Prot...
Data files: DNA-samples-publish2022-10-18_00-56.xlsx, TIS-samples-publish2022-10-11_23-37.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.SHA-220819-V1_SeqWellHughes.et.al.Master.Prot...
Data files: D.SEQ-samples-publish2022-10-25_19-32.xlsx, DNA-samples-publish2022-10-18_00-56.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.SHA-220912-V1_Drop-seq_Alignment_Cookbook.pdf
Data files: A.SCXP-samples-publish2022-10-25_21-23.xlsx, D.SEQ-samples-publish2022-10-25_19-32.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.SHA-220824-V1_P---Clustering.docx
Data files: A.SCCL-samples-publish2022-10-28_13-03.xlsx, A.SCXP-samples-publish2022-10-25_21-23.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-220824-V1_P---Immunohistochemistry-Analys...
Data files: AB-samples-publish2022-10-28_14-18.xlsx, ABP-samples-publish2022-10-28_14-25.xlsx, D.IMG-samples-publish2022-10-28_14-40.xlsx, samples-publish2023-03-21_22-232.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-220823-V1_P---PET_CT_Imaging.docx
Data files: D.IMG-samples-publish2022-10-28_13-10.xlsx, PAV-samples-publish2022-11-3_15-09.xlsx
Snapshots: No snapshots
Submitter: Jake Schissel
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.FLY-220823-V1_P---PET_CT_Imaging.docx
Data files: A.CTSC-samples-publish2022-10-28_13-14.xlsx, D.IMG-samples-publish2022-10-28_13-10.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.BOO-230324-V1_KC_Protocol
Data files: PAT-samples-publish-2024-05-21_13-17.xlsx, PAT-samples-publish2023-05-17_13-17.xlsx, PAV-samples-publish-2024-05-21_13-27.xlsx, PAV-samples-publish2023-05-17_13-27.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.BOO-230324-V1_KC_Protocol
Data files: PAV-samples-publish-2024-05-21_13-27.xlsx, PAV-samples-publish2023-05-17_13-27.xlsx, TIS-samples-publish-2024-05-21_15-05.xlsx, TIS-samples-publish2023-05-17_15-05.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.SES-230405-V1_JP_Flow_Protocol.docx
Data files: AB-samples-publish-2024-05-21_15-29.xlsx, AB-samples-publish2023-05-17_15-29.xlsx, ABP-samples-publish-2024-05-21_15-30.xlsx, ABP-samples-publish2023-05-17_15-30.xlsx, D.FCS-samples-publish-2024-05-21_12-52.xlsx, D.FCS-samples-publish2023-06-01_12-52.xlsx, D.FLOW-samples-publish-2024-05-21_11-32.xlsx, D.FLOW-samples-publish2023-06-01_11-32.xlsx, TIS-samples-publish-2024-05-21_15-05.xlsx, TIS-samples-publish2023-05-17_15-05.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: No SOPs
Data files: A.FLOW-samples-publish2023-05-17_15-39.xlsx, D.FLOW-samples-publish-2024-05-21_11-32.xlsx, D.FLOW-samples-publish2023-06-01_11-32.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-231201-V1_Study_Design-ACS-GC6.docx
Data files: samples-publish2023-12-01-PAT.xlsx, samples-publish2023-12-01-PAV.xlsx
Snapshots: No snapshots
Submitter: Charles Demurjian
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: IMPAcTB
Organisms: No organisms
SOPs: P.ALT-231201-V1_Study_Design-ACS-GC6.docx
Data files: samples-publish2023-12-01-PAV.xlsx, samples-publish2023-12-01-TIS.xlsx
Snapshots: No snapshots
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ADFP Analysis - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: All Metadata
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ADFP Analysis - Data Linked, Antibody Dependent Functional Profiling - Data ...
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ADCD Analysis - Data Linked, Antibody Dependent Complement Deposition - Data...
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ADCD Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ELISA Assay - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Short Read Sequencing - Data Linked, Single Cell Expression Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Single Cell Clustering - Data Linked, Single Cell Expression Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ELISA Assay - Data Linked, FC-Receptor Binding Assay - Data Linked, Flow Cytometry - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Flow Cytometry - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Cell Extraction - Metadata, Tissue Collection – Metadata
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Antibody Dependent Functional Profiling - Data ..., Bacterial Survivability Restriction Assay - Dat..., Cell Extraction - Metadata, Cell Sorting – Data Linked, Flow Cytometry - Data Linked, Short Read Sequencing - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Cell Sorting – Data Linked, Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Mouse Challenge – Metadata, Tissue Collection – Metadata
Batch sample publishing
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Cell Sorting – Data Linked, Mouse Challenge – Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ELISA Assay - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: ADCD Analysis - Data Linked, Antibody Dependent Complement Deposition - Data...
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Cell Extraction - Metadata, Short Read Sequencing - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Flow Cytometry - Data Linked, Flow Cytometry Analysis - Data Linked, Mouse Challenge – Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Mouse Challenge – Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Antibody-Fab and -Fc features promote Mycobacte...
Assays: Mouse Challenge – Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Systematic deconstruction of myeloid cell signa...
Assays: Library Creation - Metadata, Short Read Sequencing - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Systematic deconstruction of myeloid cell signa...
Assays: Gene Expression Analysis - Data Linked, Single Cell Expression Analysis - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Systematic deconstruction of myeloid cell signa...
Assays: Patient Visit - Metadata, Tissue Collection - Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: CITESEQ Analysis - Data Linked, Library Prep - Metadata, Short Read Sequencing - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: Model Validation - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: Histology - Data Linked
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: Pathogen Challenge and Antibody Depletion - Met..., Tissue Collection - Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: Cell Isolation - Metadata
Creator: Charles Demurjian
Submitter: Charles Demurjian
Investigations: IMPAcTB
Studies: Comparable Non-canonical T cell responses are a...
Assays: Flow Cytometry - Data Linked
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