Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-sequencing) is a multimodal highthroughput
single-cell technology that measures contemporaneously gene and surface protein expression levels
for each single cell sequenced. By using a CITE-sequencing dataset of patients infected with severe acute respiratory
syndrome ...»»»»
Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-sequencing) is a multimodal highthroughput
single-cell technology that measures contemporaneously gene and surface protein expression levels
for each single cell sequenced. By using a CITE-sequencing dataset of patients infected with severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), we aimed at developing a robust analysis pipeline that will later
serve for more ambitious purposes. Our study included the analysis of peripheral blood mononuclear cells
(PBMCs) derived from 6 COVID-19 donors (3 moderate, 3 severe) and 6 healthy donors. Our study design included
a panel of 277 Antibody-derived tags (ADTs) including 9 isotype control antibodies. To decrease confounders
and sequencing costs, samples were pooled before sequencing after being labeled using the cell hashing
technique. Cells were also designed to be demultiplexed and assigned to their donor using vireo. After a deep
quality control and extensive assessment of demultiplexing, RNA and Protein matrices were further pre-processed
by maintaining only high-quality sequenced cells and doublets removal. These underwent separate normalization
and finally integration using the Weighted Nearest Neighbored analysis. A final annotation completed this initial
analysis.^^^^
