KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-human CD45 (clone HI30) | Fluidigm | Cat#3089003; RRID: AB_2661851 |
| Mouse monoclonal anti-human CD66a/c/d/e (clone B1.1/CD66) | BD Biosciences | Cat# 551354; RRID: AB_394166 |
| Mouse monoclonal anti-human IgM (clone MHM-88) | BioLegend | Cat#314502; RRID: AB_493003 |
| Mouse monoclonal anti-human CD19 (clone HIP19) | Fluidigm | Cat#3142001; RRID: AB_2651155 |
| Mouse monoclonal anti-human CD123 (clone 6H6) | Fluidigm | Cat#3143014B, RRID: AB_2811081 |
| Mouse monoclonal anti-human CD4 (clone RPA-T4) | Fluidigm | Cat#3145001; RRID: AB_2661789 |
| Mouse monoclonal anti-human IgD (clone IA6–2) | Fluidigm | Cat#3146005B; RRID:AB_2811082 |
| Mouse monoclonal anti-human CD11c (clone Bu15) | Fluidigm | Cat#3147008; RRID:AB_2687850 |
| Mouse monoclonal anti-human CD127 (clone A019D5) | Fluidigm | Cat#3149011; RRID:AB_2661792 |
| Mouse monoclonal anti-human CD1c (clone L161) | BioLegend | Cat# 331501; RRID:AB_1088996 |
| Mouse monoclonal anti-human CD14 (clone M5E2) | Fluidigm | Cat#3175015B; RRID:AB_2811083 |
| Mouse monoclonal anti-human CD7 (clone CD7–6B7) | DVS Sciences | Cat#3153014B; RRID:AB_2811084 |
| Mouse monoclonal anti-human CD3 (clone UCHT1) | DVS Sciences | Cat#3154003B; RRID:AB_2811086 |
| Mouse monoclonal anti-human CD279/PD1 (clone EH12.2H7) | Fluidigm | Cat#3155009B; RRID:AB_2811087 |
| Mouse monoclonal anti-human CD45RA (clone HI100) | BioLegend | Cat#304102; RRID:AB_314406 |
| Mouse monoclonal anti-human FOXP3 (clone 259D/C7) | Fluidigm | Cat#3159028A; RRID:AB_2811088 |
| Rabbit monoclonal anti-human IFNAR1 (clone EP899Y) | Abcam | Cat#ab45172; RRID:AB_775764 |
| Mouse monoclonal anti-human CD16 (clone B73.1) | BioLegend | Cat#360702; RRID:AB_2562693 |
| Mouse monoclonal anti-human CD8a (clone RPA-T8) | Fluidigm | Cat#3162015; RRID:AB_2661802 |
| Mouse monoclonal anti-human CD34 (clone 581) | Fluidigm | Cat#3163014B; RRID:AB_2811091 |
| Mouse monoclonal anti-human CD45RO (clone UCHL1) | Fluidigm | Cat#3164007B; RRID:AB_2811092 |
| Mouse monoclonal anti-human CD27 (clone L128) | Fluidigm | Cat#3167006B; RRID:AB_2811093 |
| Mouse monoclonal anti-human CD25 (clone 2A3) | Fluidigm | Cat#3169003; RRID:AB_2661806 |
| Mouse monoclonal anti-human CD141 (clone M80) | BioLegend | Cat#344102; RRID:AB_2201808 |
| Mouse monoclonal anti-human CD38 (clone HIT2) | Fluidigm | Cat#3172007B; RRID:AB_2756288 |
| Mouse monoclonal anti-human GZMB (clone GB11) | Fluidigm | Cat#3173006B; RRID:AB_2811095 |
| Mouse monoclonal anti-human HLA-DR (clone L243) | Fluidigm | Cat#3174001; RRID:AB_2665397 |
| Mouse monoclonal anti-human CD56 (clone N901) | Fluidigm | Cat#3176009B; RRID:AB_2811096 |
| Mouse monoclonal anti-human COL1 (clone 5D8-G9/Col1) | ThermoFisher Scientific | Cat#CSI 008–01-02; RRID:AB_1073749 |
| Mouse monoclonal anti-human phospho-STAT4 (Tyr693) (clone 38/p-Stat4) | Fluidigm | Cat#3148006A; RRID:AB_2811098 |
| Rabbit monoclonal anti-human phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (clone D13.14.4E) | Cell Signaling Technology | Cat#4370; RRID:AB_2315112 |
| Mouse monoclonal anti-human phospho-STAT3 (Tyr705) (clone 4/P-STAT3) | Fluidigm | Cat#3158005A; RRID:AB_2811100 |
| Rabbit monoclonal anti-human phospho-STAT5 (Tyr694) (clone C11C5) | Cell Signaling Technology | Cat#9359; RRID:AB_823649 |
| Rabbit monoclonal anti-human phospho-4E-BP1 (Thr37 / Thr46) (clone 236B4) | Cell Signaling Technology | Cat#2855; RRID:AB_560835 |
| Rabbit monoclonal anti-human phospho-STAT6 (Tyr641) (clone 18) | Fluidigm | Cat#3168012A; RRID:AB_2811103 |
| Rabbit monoclonal anti-human phospho-STAT2 (Tyr690) (clone D3P2P) | Fluidigm | Cat#88410; RRID:AB_2800123 |
| Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) | Cell Signaling Technology | Cat#9167; RRID:AB_561284 |
| Mouse monoclonal anti-human CD45 (clone HI30) | Fluidigm | Cat#3089003; RRID: AB_2661851 |
|
Biological Samples | ||
| Blood from donors | The Crnic Institute Human Trisome Project Biobank | Clinicaltrials.gov Identifier: ; www.trisome.org |
|
Chemicals, Peptides, and Recombinant Proteins | ||
| Human IFNα−2a | PBL Assay Science | Cat#11100–1 |
|
Critical Commercial Assays | ||
| Cell-ID 20-Plex Pd Barcoding Kit | Fluidigm | Cat#PRD023 |
| Transcription Factor Phospho Buffer Set | BD PharMingen | Cat#563239 |
| Cell-ID Intercalator-Ir | Fluidigm | Cat#201192A |
|
Deposited Data | ||
| RNA-seq data | Espinosa lab | GEO: GSE128622 (super series), GEO: GSE128614 (unstranded data), and GEO: GSE128621 (strand-specific). |
| All flow and mass cytometry data | Espinosa lab | https://trisome.shinyapps.io/Waugh_et_al_Cell_Reports_Online_Portal/ |
| Raw CyTOF data for unstimulated samples | Espinosa lab | https://doi.org/10.17605/OSF.IO/JTE35, https://osf.io/jte35/ |
| Raw CyTOF data for stimulated samples | Espinosa lab | https://doi.org/10.17605/OSF.IO/JTE35, https://osf.io/jte35/ |
|
Software and Algorithms | ||
| FlowJo | Tree Star | v10.5.3 |
| Bead normalization of mass cytometry data | Finck et al., 2013 | https://www.cytobank.org/nolanlab |
| Combat | ‘sva’ Bioconductor package | R package v3.26.0 |
| Rtsne | Amir et al., 2013 | R package v0.13 |
| Jenson-shannon divergence | Amir et al., 2013 | |
| PhenoGraph ‘cytof_cluster’ function of cytofkit bioconductor package | Chen et al., 2016 | R package v1.12.0 |
| ‘kde2d’ function | MASS library | R package v7.3.50 |