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. 2024 Apr 26;10(10):e30314. doi: 10.1016/j.heliyon.2024.e30314
Key Resources Table
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/
HHS Vulnerability Disclosure