HCA Data Explorer

Dissecting the protein and transcriptional responses of human immune cells to T cell and monocyte specific activation

Single cell profiling is a powerful tool for studying the molecular and cellular (dys)function of activated peripheral blood mononuclear cells (PBMCs) in the context of disease. We combined CITE-seq with two levels of multiplexing (cell hashing and individuals’ genotypes) to derive a reference database of immune cell gene/protein responses to different activation conditions. PBMCs from 10 healthy adults were profiled before and after stimulating i) T cells via anti-CD3/CD28 or ii) monocytes via LPS. By using a comprehensive antibody panel (n=39) of cell type (e.g., CD16, CD14) and cell state (e.g., CD69, CD25) markers, we discovered that all lymphocytes responded to anti-CD3/CD28 stimulation, whereas LPS specifically induced inflammation in monocytes. Pseudo-temporal analyses further revealed cell- and condition-specific heterogeneity in responses to activation that were independent of individual-specific variation. Together, these data are shared within an interactive web application (https://czi-pbmc-cite-seq.jax.org/) and will serve as a resource to guide future studies of immune cell responses.

Nathan LawlorThe Jackson Laboratorynathan.lawlor@jax.org
Adam WilliamsThe Jackson LaboratoryAdam.Williams@jax.org
Duygu UcarThe Jackson LaboratoryDuygu.Ucar@jax.org
Nathan Lawlor (Computational Scientist)1
Djamel Nehar-Belaid (Computational Scientist)1
Jessica Grassmann (Experimental Scientist)1
Marlon Stoeckius (Experimental Scientist)2
Peter Smibert (Principal Investigator)2
Michael Stitzel (Principal Investigator)1
Virginia Pascual (Principal Investigator)3
Jacques Banchereau (Principal Investigator)1
Adam Williams (Principal Investigator)1
Duygu Ucar (Principal Investigator)1
1The Jackson Laboratory
2The New York Genome Center
3Weill Cornell Medicine
ami Day
Enrique Sapena Ventura
Ray Stefancsik
Marion F Shadbolt

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Analysis Portals


Project Label



Homo sapiens

Sample Type


Anatomical Entity


Organ Part


Selected Cell Types


Disease Status (Specimen)


Disease Status (Donor)


Development Stage

human adult stage

Library Construction Method


Nucleic Acid Source

single cell

Paired End


File Format

4 file formats

Cell Count Estimate


Donor Count

csv1 file(s)fastq.gz60 file(s)Rds3 file(s)xlsx1 file(s)