Computational protocol: Longitudinal dynamics of the HIV-specific B cell response during intermittent treatment of primary HIV infection

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Protocol publication

[…] PBMC were obtained by density-gradient centrifugation and cryopreserved prior to analysis. Multicolor flow cytometry was performed by using standard protocols using the following antibodies: CD3 (QD655), CD14 (QD800), CD19 (ECD), CD20 (allophycocyanin [APC]-Cy7), CD21 (Cy5PE), CD27 (QD705), CD38 (Alexa680), and IgG (BrilliantViolet421), IgD (Cy7PE), IgA (APC) and IgM (Cy55PerCP) and CXCR5 (Alexa488). Antibody labeling was performed at room temperature for 30 min. The data were collected on a LSRII flow cytometer using FACSDiva software (BD Biosciences). Color compensation was performed using single-stained samples for each fluorochrome used in addition to an unstained control. The data were further analyzed by using FlowJo software (TreeStar, Cupertino, CA). Flow cytometric cell sorting was performed on a 20-parameter FACSAria (BD), running FACSDiVa software (version 6.1.3 (BD)). HIV-specific memory B cells were identified by staining with a trimeric PE labeled YU2 gp140-foldon probe. Influenza-specific memory B cells were identified by staining with an H1-APC labeled probe. [...] Between-group analyses were performed using the nonparametric Mann-Whitney U test. Comparisons within groups were made using the Friedman test. If this yielded a significant result, further pairwise comparisons within the group were made using the Wilcoxon matched-pairs signed ranks test. Two-sided testing was done; P < .05 was considered to be statistically significant. The software used for statistical analysis was IBM SPSS statistics (version 22). […]

Pipeline specifications

Software tools FlowJo, SPSS
Applications Miscellaneous, Flow cytometry
Organisms Human poliovirus 1 Mahoney, Homo sapiens
Diseases Infection, HIV Infections