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. 2021 Jun 17;12:3727. doi: 10.1038/s41467-021-24080-1

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Overview of the STIP-Seq assay. CD4 T cells are stimulated for 24 h with PMA (162 nM)/ionomycin (1 μg/mL). Cells are fixed and permeabilized with methanol, and p24-producing cells are identified using a combination of two antibodies (KC57 and 28B7) targeting the p24 protein. p24+ cells are single-cell sorted by flow cytometry. DNA from p24+ cells is amplified by multiple displacement amplification, before performing near full-length (NFL) proviral genome sequencing, integration site analysis, TCR sequencing, and post hoc determination of the CD4 T cell memory phenotype. The illustrations of the 96-well plates were obtained from SMART (Servier Medical Art; http://smart.servier.com/), licensed under a Creative Common Attribution 3.0 Unported license (https://creativecommons.org/licenses/by/3.0/). NFL near full-length. b Representative FACS dot plots showing the KC57-FITC/28B7-APC co-staining on CD4 T cells from one HIV non-infected control, one viremic, and three ART-treated individuals.