Abstract

The main goal of this core is to establish and provide robust experimental procedures for profiling the transcriptomes and immune repertoires of tissue-resident lymphocytes. We will employ innovative methods for whole transcriptome and immune repertoire profiling in bulk populations, epigenomics, and single cell analysis. For low-input, population-level RNA-Seq we will use our recently established protocol for high-sensitivity mRNA capture and library construction. We will also provide bulk ATAC-Seq for measuring open chromatin. For single- cell RNA-Seq, we will deploy our microfluidic system for large-scale single cell capture and cDNA barcoding as well as a highly efficient plate-based method for whole transcriptome amplification. Finally, for dissecting the clonal architecture of tissue-resident T and B cells, we will provide cutting-edge methods for T cell receptor and antibody repertoire profiling.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of Allergy and Infectious Diseases (NIAID)
Type
Research Program Projects (P01)
Project #
5P01AI106697-07
Application #
9731397
Study Section
Special Emphasis Panel (ZAI1)
Project Start
Project End
Budget Start
2019-06-01
Budget End
2020-05-31
Support Year
7
Fiscal Year
2019
Total Cost
Indirect Cost

  Institution

Name
Columbia University (N.Y.)
Department
Type
DUNS #
621889815
City
New York
State
NY
Country
United States
Zip Code
10032

  Publications

Rosenfeld, Aaron M; Meng, Wenzhao; Luning Prak, Eline T et al. (2018) ImmuneDB, a Novel Tool for the Analysis, Storage, and Dissemination of Immune Repertoire Sequencing Data. Front Immunol 9:2107
Kumar, Brahma V; Connors, Thomas J; Farber, Donna L (2018) Human T Cell Development, Localization, and Function throughout Life. Immunity 48:202-213
Carpenter, D J; Granot, T; Matsuoka, N et al. (2018) Human immunology studies using organ donors: Impact of clinical variations on immune parameters in tissues and circulation. Am J Transplant 18:74-88
DeWolf, Susan; Grinshpun, Boris; Savage, Thomas et al. (2018) Quantifying size and diversity of the human T cell alloresponse. JCI Insight 3:
Senda, Takashi; Dogra, Pranay; Granot, Tomer et al. (2018) Microanatomical dissection of human intestinal T-cell immunity reveals site-specific changes in gut-associated lymphoid tissues over life. Mucosal Immunol :
Vander Heiden, Jason Anthony; Marquez, Susanna; Marthandan, Nishanth et al. (2018) AIRR Community Standardized Representations for Annotated Immune Repertoires. Front Immunol 9:2206
Chu, Coco; Moriyama, Saya; Li, Zhi et al. (2018) Anti-microbial Functions of Group 3 Innate Lymphoid Cells in Gut-Associated Lymphoid Tissues Are Regulated by G-Protein-Coupled Receptor 183. Cell Rep 23:3750-3758
Miron, Michelle; Kumar, Brahma V; Meng, Wenzhao et al. (2018) Human Lymph Nodes Maintain TCF-1hi Memory T Cells with High Functional Potential and Clonal Diversity throughout Life. J Immunol 201:2132-2140
Rosenfeld, Aaron M; Meng, Wenzhao; Chen, Dora Y et al. (2018) Computational Evaluation of B-Cell Clone Sizes in Bulk Populations. Front Immunol 9:1472
Fu, Jianing; Zuber, Julien; Martinez, Mercedes et al. (2018) Human Intestinal Allografts Contain Functional Hematopoietic Stem and Progenitor Cells that Are Maintained by a Circulating Pool. Cell Stem Cell :

Showing the most recent 10 out of 63 publications