| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Pacific blue-anti-human-CD19 (HIB19) | Biolegend | 302232 |
| PerCP-Cy5.5-anti-human-CD38 (HIT2) | BD Biosciences | 561106 |
| AF700-anti-human-CD27 (O323) | Biolegend | 302814 |
| PE-Cy7-anti-human-IgD (IA6-2) | Biolegend | 348210 |
| PE-anti-human-CD47 (REA220) | Miltenyi | 130-123-980 |
| FITC-anti-human-CD47 (REA220) | Miltenyi | 130-101-345 |
| APC-anti-human-IgA (IS11-8E10) | Miltenyi | 130-113-998 |
| Anti-human-Ig purified (polyclonal) | Thermofisher Scientific | H1700 |
| Anti-human-IgG AF488 (polyclonal) | Invitrogen | A11013 |
| Anti-human-IgA purified (polyclonal) | Jackson Immunoresearch | 109-005-011 |
| Anti-human-IgM Pacific blue (MHM-88) | Biolegend | 314513 |
| Anti-human-IgM APCCy7 (MHM-88) | Biolegend | 314520 |
| Anti-human-CD27 PE (M-T271) | BD Biosciences | 555441 |
| Anti-human-CD19 BV650 (HIB19) | Biolegend | 302237 |
| Anti-human-IgG BV510 (G18-145) | BD Biosciences | 563247 |
| Bacterial and virus strains | ||
| DENV-1 strain D1/SG/05K2916DK1/2005 | Environmental Health Institute EHI, Singapore | Genbank: EU081234.1 |
| DENV-2 strain DENV-2-TSV01 | Novartis Institute of Tropical Diseases, Singapore | Genbank: AY037116.1 |
| DENV-1 strain DENV-1-WestPac74 | Novartis Institute of Tropical Diseases, Singapore | Genbank: U88535.1 |
| Biological samples | ||
| Blood | Tan Tock Seng Hospital (TTSH), Singapore | NA |
| Chemicals, Peptides, and recombinant proteins | ||
| LIVE/DEAD stain | ThermoFisher Scientific | L34957 |
| Tetramethylrhodamine, methyl ester, Perchlorate | ThermoFisher Scientific | T668 |
| Mito Tracker™ Green | ThermoFisher Scientific | M7514 |
| TetraMethylBenzidine (TMB) | Sigma Aldrich (Merck) | 54,827-17-7 |
| Resiquimod (R848) | InVivogen | tltl-r848 |
| IL-2 | Prospecbio | CYT-209 |
| KLH | Sigma Aldrich (Merck) | 9013-72-3 |
| Critical commercial assays | ||
| SD BIOLINE dengue duo kit for NS1 detection | Abbott | 11FK46 |
| PanBio dengue IgG indirect ELISA | Abbott | 01PE30 |
| OneStep RT-PCR kit | Qiagen | 210210 |
| Protein G mag sepharose | Cytiva (formerly GE Healthcare) | 28951379 |
| Alexa Fluor™ 488 antibody labeling kit from | ThermoFisher Scientific | A20181 |
| Chromium single cell 5′ library and gel bead kit | Research Instrument – 10X genomics | 1000014 |
| Chromium single cell V(D)J enrichment kit, human B cell | Research Instrument – 10X genomics | 1000016 |
| Chromium single cell 3’/5′ library construction kit | Research Instrument – 10X genomics | 1000020 |
| Chromium i7 multiplex kit | Research Instrument – 10X genomics | 120262 |
| Chromium single cell a chip kit | Research Instrument – 10X genomics | 1000009 |
| PicoPure™ RNA isolation kit | ThermoFisher Scientific | KIT0204 |
| Nextera XT DNA library preparation kit | Illumina Singapore | FC-131-1096 |
| Nextera XT index kit v2 | Illumina Singapore | FC-131-2001 FC-131-2002 FC-131-2003 FC-131-2004 |
| Experimental models: Cell lines | ||
| Vero cells | ATCC | ATCC® CCL-81™ |
| HEK293-6E | National Research Council of Canada | NRC file 11,565 |
| Oligonucleotides | ||
| GAACATGGRACAAYTGCAACYAT | Integrated DNA Technologies | DENV-1 D1MGBEn469s-forward |
| CCGTAGTCDGTCAGCTGTATTTCA | Integrated DNA Technologies | DENV-1 D1MGBEn536r-reverse |
| ACACCACAGAGTTCCATCACAGA | Integrated DNA Technologies | DENV-2 Den 2.2F |
| CATCTCATTGAAGTCNAGGCC | Integrated DNA Technologies | DENV-2 Den 2.2R |
| ATGAGATGYGTGGGAGTRGGAAAC | Integrated DNA Technologies | DENV-3 D3MGBEn1sFWD |
| CAC CAC DTC AAC CCA CGT AGC T | Integrated DNA Technologies | DENV-3 D3MGBEn71rREV |
| GGTGACRTTYAARGTHCCTCAT | Integrated DNA Technologies | DENV-4 D4TEn711sFWD |
| WGARTGCATRGCTCCYTCCTG | Integrated DNA Technologies | DENV-4 D4TEn786cREV |
| GARAGACCAGAGATCCTGCTGTCT | Integrated DNA Technologies | DENV-1 to 4 DV1-4_realt_fwd |
| ACCATTCCATTTTCTGGCGTT | Integrated DNA Technologies | DENV-1 to 4 DV1-4_realt_rev |
| CAG CTC CCG GAC TGA CTG | Integrated DNA Technologies | ALDOA_fwd |
| ATT CCA CGG GCT AGA GGA G | Integrated DNA Technologies | ALDOA_rev |
| GGC AAT GAC GAA GGA GGT TA | Integrated DNA Technologies | CD47_fwd |
| ATC CGG TGG TAT GGA TGA GA | Integrated DNA Technologies | CD47_rev |
| AGA AGG AAG AAA GGG CAG ACT T | Integrated DNA Technologies | CYCS_fwd |
| GGC AGT GGC CAA TTA TTA CTC a | Integrated DNA Technologies | CYCS_rev |
| AGT CAA AGA TCT CCC TGG CA | Integrated DNA Technologies | ENO1_fwd |
| TAC GTT CAC CTC GGT GTC TG | Integrated DNA Technologies | ENO1_rev |
| GCA AAT TCC ATG GCA CCG T | Integrated DNA Technologies | GAPDH_fwd |
| TCG CCC CAC TTG ATT TTG G | Integrated DNA Technologies | GAPDH_rev |
| CTT TGC TTT CCT TGG TCA GG | Integrated DNA Technologies | HPRT_fwd |
| CAA GGG CAT ATC CTA CAA CAA AC | Integrated DNA Technologies | HPRT_rev |
| CAG GTG TTC CAG AGC GAG TT | Integrated DNA Technologies | NDUFB2_fwd |
| TAC GGA AAG TGA CCC AGC AC | Integrated DNA Technologies | NDUFB2_rev |
| TAG GGC TGA GGT TTG TCC AG | Integrated DNA Technologies | SOD2_fwd |
| CAC CGA GGA GAA GTA CCA GG | Integrated DNA Technologies | SOD2_rev |
| GGC GAA GTC GAT ATA GGC AG | Integrated DNA Technologies | TPI1_fwd |
| AGT TCT TCG TTG GGG GAA AC | Integrated DNA Technologies | TPI1_rev |
| TAC GTC CCA GGA GAT GGA GA | Integrated DNA Technologies | UCP2_fwd |
| CCG TGA ACC TTA CAA AGC C | Integrated DNA Technologies | UCP2_rev |
| AAG CAG TGG TAT CAA CGC AGA GTA CAT rGrG + G | Integrated DNA Technologies | TSO |
| AAG CAG TGG TAT CAA CGC AGA GTA CT30V N | Integrated DNA Technologies | Oligo-dT30VN |
| AAG CAG TGG TAT CAA CGC AGA GT | Integrated DNA Technologies | ISPCR oligo |
| Deposited data | ||
| Human reference genome - release 22 (GRCh38.p2) | GENCODE | https://www.gencodegenes.org/human/release_22.html |
| Dataset GSE6691 | Gutiérrez et al. (2007) (Gutiérrez et al., 2007) | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE6691 |
| Dataset GSE172180 | This study | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172180 |
| Software and algorithms | ||
| FlowJo_v10 software | Tree Star | https://www.flowjo.com/ |
| scPred | Alquicira-Hernandez J et al., 2019 (Alquicira-Hernandez et al., 2019) | https://github.com/powellgenomicslab/scPred |
| Seurat | Butler et al., 2018 (Butler et al., 2018) | https://satijalab.org/seurat/ |
| Fluidigm’s SINGuLAR toolset v3.5.2 | N/A | https://www.fluidigm.com/software |
| Ingenuity Pathway Analysis (IPA) | N/A | https://www.qiagenbioinformatics.com/products/ingenuity-pathway-analysis |
| BASIC: BCR assembly from single cells | Canzar et al., 2017(Canzar et al., 2017) | http://ttic.uchicago.edu/∼aakhan/BASIC |
| MiXCR version 1.8.2 | Bolotin et al., 2015 (Bolotin et al., 2015) | https://github.com/milaboratory/mixcr |
| VDJtools | Shugay M et al., 2015 (Shugay et al., 2015) | https://vdjtools-doc.readthedocs.io/ |
| Gene set enrichment analysis v4.0.3 | Subramanian et al., 2005 (Subramanian et al., 2005) | https://www.gsea-msigdb.org/gsea/index.jsp |
| Connectivity Map (CMap) | Lamb et al., 2006 (Lamb et al., 2006) | https://clue.io/cmap |
| RSEM program version 1.2.19 | Li and Dewey, 2011 (Li and Dewey, 2011) | https://github.com/deweylab/RSEM |
| Harmony program | Korsunsky et al., 2019 (Korsunsky et al., 2019) | https://github.com/immunogenomics/harmony |
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