REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Antibodies | ||
Brilliant Violet 510TM anti-human CD3 Antibody | Biolegend | Cat#; 317,332 RRID: AB_2561943 |
APC anti-human CD19 | Immunotools | Cat#; 302,816 RRID: AB_571977 |
APC/Cyanine 7 anti-human CD27 Antibody | Biolegend | Cat#; 302,816 RRID: AB_571977 |
PerCP anti-human CD38 Antibody | Biolegend | Cat#; 303,520 RRID: AB_893313 |
FITC anti-human CD138 (Syndecan-1) Antibody | Biolegend | Cat#; 352,304 RRID: AB_10900441 |
PE anti-human/mouse Cutaneous Lymphocyte Antigen (CLA) Antibody | Biolegend | Cat#321312; RRID: AB_2565589 |
Biological Samples | ||
Human PBMC samples | The Institutional Review Boards of Faculty of Medicine Vajira Hospital (No.015/12), Faculty of Tropical Medicine Mahidol University (TMEC 13041), and Faculty of Medicine, Ramathibodi Hospital, Mahidol University (MURA2016/219 and MURA2019/603), as part of the DENFREE initiative (https://cordis.europa.eu/project/id/282378/results) | N/A |
Deposited Data | ||
Dataset: Processed 3′ scRNA-seq datasets of dengue PBMC samples | Arora et al. (2023) | https://data.mendeley.com/datasets/6ry3x7r8hf/3 |
Dataset: Quantification matrices of 5′ scRNA-seq and scBCR sequencing of primary and secondary dengue PBMC samples | Waickman et al. | Gene Expression Omnibus (GEO): GSE145307 |
Dataset: Processed 3′ scRNA-seq datasets of COVID-19 PBMC samples | Schulte-Schrepping et al. | http://fastgenomics.org |
Processed scRNA-seq datasets of B cell populations used in this study | Mendeley Data | -https://data.mendeley.com/datasets/xmnp8c5c65/1 |
Software and Algorithms | ||
RStudio v3.1.4 | RStudio | https://www.rstudio.com/ |
Seurat v3.1.2 | (Stuart et al., 2019) | https://satijalab.org/seurat/ |
ggplot2 v3.3.2 | (Wickham, 2016) | https://ggplot2.tidyverse.org/ |
Scanpy v1.9.1 | (Wolf et al., 2018) | https://scanpy.readthedocs.io/en/stable/index.html# |
BBKNN | (Polański et al., 2019) | https://github.com/Teichlab/bbknn |
Scirpy v1.8.0 | (Sturm et al., 2020) | https://scirpy.scverse.org/en/latest/ |
Flowjo v10.8.1 | TreeStar Inc | https://www.flowjo.com/ |