METHODS article
Front. Bioinform.
Sec. Single Cell Bioinformatics
Volume 5 - 2025 | doi: 10.3389/fbinf.2025.1630161
This article is part of the Research TopicAI in Single-Cell BiologyView all articles
Quantitative measures to assess the quality of Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) data
Provisionally accepted
- 1University of Pittsburgh, Pittsburgh, United States
- 2Northeastern University, Boston, United States
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Background: Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) is a powerful technique to simultaneously measure the gene expression and cell surface protein abundances in individual cells. To discover accurate and reliable biological findings from CITE-Seq data, it is critical to control the quality (QC) of CITE-Seq data. However, no public method has been developed for CITE-Seq QC.Results: In this manuscript, we propose the first software package for multi-layered, systemic, and quantitative quality control (CITESeQC). Recognizing the multi-layer nature of CITE-Seq data, CITESeQC performs QC across gene expression, surface protein, and their interactions. It systemically evaluates all genes and protein markers assayed in the data and filters out some of them based on individual quality measures. Also, for quantitative QC that allows for objective and standardized analyses, CITESeQC quantifies cell type-specific expression of genes and surface proteins using Shannon entropy and correlation-based measures. Lastly, for wide applicability, CITESeQC will guide users through a simple process that results in a full markdown report with supporting figures and explanations with minimal intervention from the user. Conclusions: By ensuring the quality of CITE-Seq data, CITESeQC will help accurately and reliably identify not only the gene expression characteristics in each cell type but also cell types with certain surface protein markers for further clinical application.
Keywords: CITE-seq, Quality control, multi-layered QC, systemic QC, quantitative QC
Received: 17 May 2025; Accepted: 29 Jul 2025.
Copyright: © 2025 Sun, Morrison, Kim, Yan and Park. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Hyun Jung Park, University of Pittsburgh, Pittsburgh, United States
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