KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Antibodies used for CyTOF are summarized in Table S2 | ||
| Anti-human CCR5 (clone NP-6G4) | Fluidigm | Cat# 3156015A; RRID:AB_2661814 |
| Anti-human SIGLEC1(clone 7–239) | Biolegend | Cat# 346002; RRID:AB_2189031 |
| Anti-human CXCR3 (cloneG025H7) | Biolegend | Cat# 353702; RRID:AB_353702 |
| Anti-human CD45RA (clone HI130) | Biolegend | Cat# 304002; RRID:AB_2661811 |
| Anti-human Eotaxin | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human Flt.3L | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL5 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human MCP1 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD19 (clone HIB19) | Biolegend | Cat# 302202; RRID:AB_2661817 |
| Anti-humanBDCA1 (clone L161) | Biolegend | Cat# 331502; RRID:AB_2661820 |
| Anti-humanPD1(clone EH12.2H7) | Biolegend | Cat# 329902; RRID:AB_940488 |
| Anti-human CD24 (clone ML5) | Biolegend | Cat# 311102; RRID:AB_314851 |
| Anti-human CCR4 (clone 205410) | R&D Systems | Cat# MAB1567; RRID:AB_2074395 |
| Anti-human GCSF | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human MCP3 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL1A | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human TNFa | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human VEGF | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD11c (clone Bu15) | Biolegend | Cat# 301616; RRID:AB_439736 |
| Anti-human CD45RA (clone HI100) | Biolegend | Cat# 304102; RRID:AB_314406 |
| Anti-human CD127 (clone A019D5) | Biolegend | Cat# 351302; RRID:AB_10718513 |
| Anti-human CEACAM8 (clone G10F5) | Biolegend | Cat# 305102; RRID:AB_2661823 |
| Anti-human IFNg | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL12p70 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL1RA | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL9 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL4 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IP10 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD56 (clone B159) | BD Biosciences | Cat# 555513; RRID:AB_2661829 |
| Anti-human CD161(clone HP-3G10) | Biolegend | Cat# 339902; RRID:AB_2661837 |
| Anti-human EGF | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human TGFa | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human GRO | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human MDC | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL13 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL6 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human MIP1a | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human MIP1b | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human TNFb | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD4 (clone RPA-T4) | Biolegend | Cat# 300502; RRID:AB_314070 |
| Anti-human CD8 (clone RPA-T8) | Biolegend | Cat# 301002; RRID:AB_2661818 |
| Anti-human CXCR5 (clone J252D4) | Biolegend | Cat# 356902; RRID:AB_2561811 |
| Anti-human CD38 (clone HB-7) | Biolegend | Cat# 356602; RRID:AB_2661836 |
| Anti-human IFNa | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human sCD40L | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human RANTES | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD27 (clone O323) | Biolegend | Cat# 302802; RRID:AB_2661825 |
| Anti-human CCR6 (clone G034E3) | Biolegend | Cat# 353402; RRID:AB_10918625 |
| Anti-human Fractalkine | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL10 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL12p40 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human PDGF AA BB | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL17 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL8 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human THBD (clone M80) | Biolegend | Cat# 344102; RRID:AB_2201808 |
| Anti-human IL2RA (clone M-A251) | Biolegend | Cat# 356102; RRID:AB_2661833 |
| Anti-human CD3 (clone UCHT1) | Biolegend | Cat# 300402; RRID:AB_2661835- |
| Anti-human CXCR3 (clone 2A9–1) | Biolegend | Cat# 341602; RRID:AB_1595422 |
| Anti-human AXL (clone 108724) | R&D Systems | Cat# MAB154; RRID:AB_2062558 |
| Anti-human GMCSF | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human PDGF AA | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human CD57 (clone HCD57) | Biolegend | Cat# 322302; RRID:AB_2661815 |
| Anti-human CD20 (clone 2H7) | Fluidigm | Cat# 3147001B |
| Anti-human CD123 (clone 6H6) | Biolegend | Cat# 306002; RRID:AB_2661822 |
| Anti-human FGF2 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL15 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL1b | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL2 | Millipore Corp | Cat# HSTCMAG-28SK |
| Anti-human IL7 | Millipore Corp | Cat# HSTCMAG-28SK |
| Biological Samples | ||
| PAXgene samples from humans | Dengue pediatric cohort study in Nicaragua | Accession number: SDY1476 https://www.immport.org/home |
| Serum samples from humans | Dengue pediatric cohort study in Nicaragua | Accession number: SDY1476 https://www.immport.org/home |
| PBMCs samples from humans | Dengue pediatric cohort study in Nicaragua | Accession number: SDY1476 https://www.immport.org/home |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Histopaque-1077 | Sigma | Cat# 10771 |
| Fetal bovine serum Premium US source | Thomas scientific | Cat# 1005837 |
| Phosphate buffered saline (PBS) GIBCO | Sigma | Cat# P5119 |
| 10,000 U Penicillin-Streptomycin | Sigma | Cat# P4333 |
| Dimethyl sulfoxide | Sigma | Cat# C6164 |
| Cell-ID Intercalator-Rh—500 μM | Fluidigm | Cat# 201103A |
| EDTA | Sigma | Cat# E6758 |
| Cell-ID Intercalator-Ir—125 μM | Fluidigm | Cat# 201192A |
| EQ Four Element Calibration Beads— 100 mL | Fluidigm | Cat# 201078 |
| Formaldehyde solution | Sigma-Aldrich | Cat# 252549 |
| Molecular grade water | Thermo Fisher | Cat# Am9935 |
| RPMI-1640 | Sigma | Cat# R7388 |
| Benzonase Nuclease | Millipore | Cat# E1014 |
| Critical Commercial Assays | ||
| MILLIPLEX MAP Human High Sensitivity Cytokine Panel | Millipore Corp | HSTCMAG-28SK |
| TrueSeq RNA CD Index Plate (96 Indexes, 96 samples) | Illumina | Cat# 20019792 |
| TruSeq Total Stranded RNA HT kit (w/Ribo-Zero Globin) | Illumina | Cat# 20020612 |
| Paxgene Blood RNA Kit | QIAGEN | Cat# 762164 |
| RNeasy MinElute Cleanup kit | QIAGEN | Cat# 74204 |
| Qubit RNA High Sensitivity Assay kit | Thermo Fisher | Cat# Q32852 |
| RNA ScreenTapes | Agilent | Cat# 5067-5576 |
| D1000 ScreenTapes | Agilent | Cat# 5067-5582 |
| Superscript II | Invitrogen | Cat# 18-064-022 |
| KAPA Library Quantification Kit Illumina | Kapa Biosystems | Cat# 79960298001 |
| HiSeq 3000/4000 paired-end cluster kit | Illumina | Cat# PE410-1001 |
| HiSeq 3000/4000 SBS kit | Illumina | Cat# FC410-1003 |
| Agencourt AMPure XP beads system | Beckman Coulter | Cat# A63881 |
| Cell-ID 20-Plex Pd Barcoding Kit | Fluidigm | Cat# 201060 |
| MAXPAR X8 Multimetal labeling kit | Fuidigm | Cat# 201300 |
| Deposited Data | ||
| RNA-seq transcript and gene data | This study | https://www.ncbi.nlm.nih.gov/geo Accession number: GEO: GSE12982 and https://www.immport.org/home “Immport: SDY1476” |
| Luminex data | This study | https://www.immport.org/home “Immport: SDY1476” |
| CyTOF data | This study | https://www.immport.org/home “Immport : SDY1476” https://flowrepository.org/: FR-FCM-Z2HQ |
| Software and Algorithms | ||
| CyTOF analysis | Cytobank | https://www.cytobank.org/ |
| XMap Platform | Luminex Corporation | https://www.luminexcorp.com/xmap-technology |
| PlateDesigner | Suprun and Suaréz Fariñas, 2019 | platedesigner.net |
| xPONENT Multiplex analysis software | Luminex corporation | https://www.luminexcorp.com/xponent/ |
| RNA -preprocessing reads FASTQC | FASTQC | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| RNA-preprocessing tool FASTAX Toolkit | Kim et al., 2015a | (http://hannonlab.cshl.edu/fastx_toolkit/ version 0.11.4 |
| HISAT 2 | Kim et al., 2015b | http://daehwankimlab.github.io/hisat2/ (version 2.0.4) |
| SAMtools | Li et al., 2009 | http://samtools.sourceforge.net/ (version 0.1.19) |
| StringTie | Pertea et al., 2015 | https://ccb.jhu.edu/software/stringtie/ (version 1.2.2) |
| Python | prepDE.py | https://www.python.org/ |
| EnrichR platform | Chen et al., 2013; Fabregat et al., 2016; Mi et al., 2013) | https://amp.pharm.mssm.edu/Enrichr/ |
| Gene Ontology (GO) biological process | The Gene Ontology Consortium, 2019; Ashburner et al., 2000 | http://geneontology.org/ |
| Panther | Panther, 2016 | http://www.pantherdb.org/ |
| Reactome | Reactome, 2016 | https://reactome.org/ |
| WikiPathways | WikiPathways, 2016 | https://www.wikipathways.org/index.php/WikiPathways |
| R studio | R project | https://www.r-project.org/ (version 3.5.0) |
| voom | Law et al., 2014 | https://rdrr.io/bioc/limma/man/voom.html |
| KEGG | Luo and Brouwer, 2013; Ogata et al., 1999 | https://www.genome.jp/kegg/annotation/ |
| limma | Smyth et al., 2005 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| WGCNA | Zhang and Horvath, 2005 | https://cran.r-project.org/web/packages/WGCNA/index.html (version 1.51) |
| coexpp | Zhang and Horvath, 2005 | (version 0.1.0, https://bitbucket.org/multiscale/coexpp) |
| ForceAtlas2 algorithm | Bastian and Heymann, 2009, Int. Assoc. Adv. Artif. Intell. Conf. Weblogs Soc. Media, conference | https://github.com/gephi/gephi/wiki/Force-Atlas-2 Gephi (version 0.9.1) |
| Cytoscape | Bastian and Heymann, 2009, Int. Assoc. Adv. Artif. Intell. Conf. Weblogs Soc. Media, conference; Smoot et al., 2011 | https://cytoscape.org/ (version 3.4.0) |
| corrplot | R-project | https://cran.r-project.org/web/packages/corrplot/vignettes/corrplot-intro.html |
| clusterCrit R | R-project | https://cran.r-project.org/web/packages/clusterCrit/index.html (version 1.2.7). |
| Dendextend R package | R-project | https://cran.r-project.org/web/packages/dendextend/index.html |
| glmnet R package | Friedman et al., 2010 | https://cran.r-project.org/web/packages/glmnet/index.html (version 2.0-5) |