biostudies-literatureVallejo JNCATS NIH HHSNational Institutes of Health GrantNIAID NIH HHSNHLBI NIH HHSCancer Research InstituteSwedish Society for Medical Research193https://www.ebi.ac.uk/biostudies/studies/S-EPMC9434837biostudies-literatureUnknown20(1)<h4>Background</h4>Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single-cell (sc)RNA sequencing (scRNA-seq) in PBMCs.<h4>Results</h4>Among 31 participants in the Women's Interagency HIV Study (WIHS), we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs (tool for visualizing high-dimensional data) and Louvain clustering, we identified 50 subsets among CD4+ T, CD8+ T, B, NK cells, and monocytes. This resolution was superior to flow cytometry, mass cytometry, or scRNA-seq without antibodies. Combined protein and transcript scRNA-seq allowed for the assessment of disease-related changes in transcriptomesBMC biologyCombined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells.PMC9434837R01 HL148094P30 AI050410U01-AI-103390K01 HL137557U01-AI-034989U01 HL146204U01 HL146202R35 HL145241R01 HL140976P01 HL136275R01 HL126543U01 AI103408R01 HL121697P30 AI027767R01 HL134236U01 AI034989U01 AI031834R35-HL-145241, R01-HL-121697, R01-HL-148094UL1 TR000004P30 AI050409U01 AI103390U01-AI-103408R01-HL-126543, 5R01-HL-126543-05, 5R01-HL-140976-02, R01-HL-148094-01, R01-HL-148094K01-HL-137557P01-KL-136275, R01-HL-134236Durant CPLanier LLHedrick CCAlimadadi AGhosheh YOfotokun IVallejo JPattarabanjird TShemesh ARoy PWeber KMTracy RPArmstrong Suthahar SSHeath SLAdimora AALanday ALMcNamara CAGulati RTien PCSaigusa RSuryawanshi VLey KHanna DBHodis HNEhinger ELazar JMMack WJKaplan RCfalseCombined protein and transcript single-cell RNA sequencing in human peripheral blood mononuclear cells.<h4>Background</h4>Cryopreserved peripheral blood mononuclear cells (PBMCs) are frequently collected and provide disease- and treatment-relevant data in clinical studies. Here, we developed combined protein (40 antibodies) and transcript single-cell (sc)RNA sequencing (scRNA-seq) in PBMCs.<h4>Results</h4>Among 31 participants in the Women's Interagency HIV Study (WIHS), we sequenced 41,611 cells. Using Boolean gating followed by Seurat UMAPs (tool for visualizing high-dimensional data) and Louvain clustering, we identified 50 subsets among CD4+ T, CD8+ T, B, NK cells, and monocytes. This resolution was superior to flow cytometry, mass cytometry, or scRNA-seq without antibodies. Combined protein and transcript scRNA-seq allowed for the assessment of disease-related changes in transcriptomes2022-01-01T00:00:00Z2022 Sep2025-04-19T18:51:36.958Z2025-04-19T18:51:36.958ZS-EPMC94348373604534310.1186/s12915-022-01382-4