HCA Data Explorer

A single-cell reference map of transcriptional states for human blood and tissue T cell activation

Human T cells coordinate adaptive immunity in diverse anatomic compartments through production of cytokines and effector molecules, but it is unclear how tissue site influences T cell persistence and function. Here, we use single cell RNA-sequencing (scRNA-seq) to define the heterogeneity of human T cells isolated from lungs, lymph nodes, bone marrow and blood, and their functional responses following stimulation. Through analysis of >50,000 resting and activated T cells, we reveal tissue T cell signatures in mucosal and lymphoid sites, and lineage-specific activation states across all sites including distinct effector states for CD8+ T cells and an interferon-response state for CD4+ T cells. Comparing scRNA-seq profiles of tumor-associated T cells to our dataset reveals predominant activated CD8+ compared to CD4+ T cell states within multiple tumor types. Our results therefore establish a high dimensional reference map of human T cell activation in health for analyzing T cells in disease.

Donna L FarberColumbia University Irving Medical Centerdf2396@cumc.columbia.edu
Peter A SimsColumbia University Irving Medical Centerpas2182@cumc.columbia.edu
Hanna Mendes Levitin (Computational Scientist)1
Peter A Szabo (Experimental Scientist)1
Michelle Miron1
Mark E Snyder1
Takashi Senda1
Jinzhou Yuan1
Yim Ling Cheng1
Erin C Bush1
Pranay Dogra1
Puspa Thapa1
Donna L Farber (Principal Investigator)1
Peter A Sims (Principal Investigator)1
1Columbia University Irving Medical Center
Chris Villarreal

To reference this project, please use the following link:

GEO Series Accessions:

For information regarding data sharing and data use, please see our Data Access Policy.

Analysis Portals


Project Label



Homo sapiens

Sample Type


Anatomical Entity

4 anatomical entities

Organ Part

4 organ parts

Selected Cell Types

4 cell types

Disease Status (Specimen)


Disease Status (Donor)

2 disease statuses

Development Stage

human adult stage

Library Construction Method

10x 3' v2

Nucleic Acid Source

single cell

Paired End


File Format

6 file formats

Cell Count Estimate


Donor Count

bam16 file(s)csv4 file(s)fastq.gz32 file(s)loom20 file(s)tar1 file(s)xlsx1 file(s)