Appendix 1—key resources table.
| Reagent type (species) or resource | Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Cell line (M. musculus) | OP9-DL1 | Schmitt, T. M. & Zúñiga-Pflücker, J. C. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17, 749–756 (2002). | No identifier, but similar to RCB Cat# RCB2927, RRID:CVCL_B220 |
Provided by Prof. Dr. Zúñiga-Pflücker, University of Toronto |
| Cell line (M. musculus) | OP9 | Kodama, H., Nose, M., Niida, S. & Nishikawa, S. Involvement of the c-kit receptor in the adhesion of hematopoietic stem cells to stromal cells. Exp. Hematol. 22, 979–984 (1994). | No identifier, but similar to RCB Cat# RCB2926, RRID:CVCL_B219 |
Provided by Prof. Dr. Zúñiga-Pflücker, University of Toronto |
| Cell line (H. sapiens) | Raji | ATCC | ATCC Cat# CRL-7936, RRID:CVCL_0511 | Cell line maintained in lab |
| Cell line (H. sapiens) | K562 | ATCC | ATCC Cat# CCL-243, RRID:CVCL_0004 | Cell line maintained in lab |
| Biological sample (H. sapiens) | ILC1-like cells; CB ILC1-like cells |
Freshly isolated from donated umbilical cord blood (CB) within the lab | José Carreras Stem Cell Bank at the ITZ, University Hospital Düsseldorf | |
| Biological sample (H. sapiens) | ILC2; CB ILC2 |
Freshly isolated from donated umbilical cord blood (CB) within the lab | José Carreras Stem Cell Bank at the ITZ, University Hospital Düsseldorf | |
| Biological sample (H. sapiens) | CD56bright NK cells; CB CD56bright NK cells | Freshly isolated from donated umbilical cord blood (CB) within the lab | José Carreras Stem Cell Bank at the ITZ, University Hospital Düsseldorf | |
| Biological sample (H. sapiens) | CB MNCs (mono nuclear celLs) | Freshly isolated from donated umbilical cord blood (CB) within the lab | José Carreras Stem Cell Bank at the ITZ, University Hospital Düsseldorf | |
| Biological sample (H. sapiens) | ILC1-like; PB ILC1-like cells |
Freshly isolated from healthy blood donors in the lab | Blutspendezentrale at the University Hospital Düsseldorf | |
| Biological sample (H. sapiens) | CD56bright NK cells; PB CD56bright NK cells | Freshly isolated from healthy blood donors in the lab | Blutspendezentrale at the University Hospital Düsseldorf | |
| Antibody | anti- CD3-FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 300405, RRID:AB_314059 | “1:100” |
| Antibody | anti- CD3- BV510 (Mouse monoclonal) | Biolegend | BioLegend Cat# 300447, RRID:AB_2563467 | “1:200” |
| Antibody | anti-CD1a -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 300104, RRID:AB_314018 | “1:25” |
| Antibody | anti-CD14- FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 325604, RRID:AB_830677 | “1:100” |
| Antibody | anti-CD19 -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 302206, RRID:AB_314236 | “1:200” |
| Antibody | anti-TCRαβ-FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 306705, RRID:AB_314639 | “1:100” |
| Antibody | anti-TCRγδ -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 331207, RRID:AB_1575111 | “1:12.5” |
| Antibody | anti-CD123 -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 306014, RRID:AB_2124259 | “1:200” |
| Antibody | anti-CD303 (BDCA-2) -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 354208, RRID:AB_2561364 | “1:25” |
| Antibody | anti- FcɛR1α -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 334608, RRID:AB_1227653 | “1:25” |
| Antibody | anti-CD235α -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 349104, RRID:AB_10613463 | “1:100” |
| Antibody | anti-CD66b -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 305104, RRID:AB_314496 | “1:100” |
| Antibody | anti-CD34 -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 343504, RRID:AB_1731852 | “1:100” |
| Antibody | anti-CD94 -APC (Mouse monoclonal) | Biolegend | BioLegend Cat# 305508, RRID:AB_2133129 | “1:100” |
| Antibody | anti-CD94- PE/Cy7 (Mouse monoclonal) | Biolegend | BioLegend Cat# 305516, RRID:AB_2632753 | “1:100” |
| Antibody | anti-CD56-APC/Cy7 (Mouse monoclonal) | Biolegend | BioLegend Cat# 318332, RRID:AB_10896424 | “1:100” |
| Antibody | anti-CD56- BV650(Mouse monoclonal) | Biolegend | BioLegend Cat# 318344, RRID:AB_2563838 | “1:100” |
| Antibody | anti-CD56-PE/Dazzle594 (Mouse monoclonal) | Biolegend | BioLegend Cat# 318348, RRID:AB_2563564 | “1:100” |
| Antibody | anti-CD117-PE (Mouse monoclonal) | Biolegend | BioLegend Cat# 313204, RRID:AB_314983 | “1:100” |
| Antibody | anti-CD117 BV421 (Mouse monoclonal) | Biolegend | BioLegend Cat# 313216, RRID:AB_11148721 | “1:100” |
| Antibody | anti-CRTH2 -PE/Dazzle 594 (Rat monoclonal) | Biolegend | BioLegend Cat# 350126, RRID:AB_2572053 | “1:40” |
| Antibody | anti-CD161 -Alexa Flour (Mouse monoclonal) | Biolegend | BioLegend Cat# 339942, RRID:AB_2565870 | “1:25” |
| Antibody | anti-CD5 -APC/Cy7 (Mouse monoclonal) | Biolegend | BioLegend Cat# 364010, RRID:AB_2564506 | “1:100” |
| Antibody | anti-CD6 -PE (Mouse monoclonal) | Biolegend | BioLegend Cat# 313906, RRID:AB_2260227 | “1:100” |
| Antibody | anti-CD158b1,b2,j; KIR2DL2/L3/S2-FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 312604, RRID:AB_2296486 | “1:100” |
| Antibody | anti-CD158b1,b2,j; KIR2DL2/L3/S2-PE (Mouse monoclonal) | Biolegend | BioLegend Cat# 312606, RRID:AB_2130554 | “1:100” |
| Antibody | anti-CD158e1; KIR3DL1 - Alexa Flour (Mouse monoclonal) | Biolegend | BioLegend Cat# 312712, RRID:AB_2130824 | “1:400” |
| Antibody | anti-CD158e1; KIR3DL1 – PE (Mouse monoclonal) |
Biolegend | BioLegend Cat# 312708, RRID:AB_2249498 | “1:100” |
| Antibody | anti- CD158a,h,g; KIR2DL1/S1/S3/S5 -FITC (Mouse monoclonal) |
Biolegend | BioLegend Cat# 339504, RRID:AB_2130378
|
“1:100” |
| Antibody | anti- CD158a,h,g; KIR2DL1/S1/S3/S5 -PE (Mouse monoclonal) |
Biolegend | BioLegend Cat# 339506, RRID:AB_2130374 | “1:100” |
| Antibody | anti-IFNγ -PE/Cy7 (Mouse monoclonal) | Biolegend | BioLegend Cat# 506518, RRID:AB_2123321 | “1:20” |
| Antibody | anti-CCR4 -APC (Mouse monoclonal) | Biolegend | BioLegend Cat# 359408, RRID:AB_2562429 | “1:100” |
| Antibody | anti-CD107a -FITC (Mouse monoclonal) | Biolegend | BioLegend Cat# 328606, RRID:AB_1186036 | “1:200” |
| Antibody | anti-Mouse -PE (Goat polyclonal) | Biolegend | BioLegend Cat# 405307, RRID:AB_315010 | “1:250” |
| Antibody | anti-CD127 -PE/Cy5 (Mouse monoclonal) | Beckman Coulter | Beckman Coulter Cat# A64617, RRID:AB_2833010 | “1:40” |
| Antibody | anti-CD28 -PE (Mouse monoclonal) | Beckman Coulter | Beckman Coulter Cat#IM2071U, RRID:AB_2833011 | “1:10” |
| Antibody | anti-NKG2A -APC (Mouse monoclonal) | Beckman Coulter | Beckman Coulter Cat# A60797, RRID:AB_10643105 (conjugate APC) | “1:100” |
| Antibody | anti-CD158b2; KIR2DL3 -FITC (Mouse monoclonal) | R&D | R and D Systems Cat# FAB2014F-100, RRID:AB_2833013 | “1:20” |
| Antibody | anti-CCR9 (Mouse monoclonal) | R&D | R and D Systems Cat# MAB1791, RRID:AB_2073268 | “1:100” caution only stable for 4 month |
| Antibody | anti- CCR7 -PE-CF594 (Mouse monoclonal) | BD Bioscience | BD Biosciences Cat# 562381, RRID:AB_11153301 | “1:20” |
| Antibody | anti-Tbet -BV605 (Mouse monoclonal) | Biolegend | BioLegend Cat# 644817, RRID:AB_11219388 | “1:20” |
| Antibody | anti- Eomes-PE-eFlour610 (Mouse monoclonal) | Invitrogen | Thermo Fisher Scientific Cat# 61-4877-42, RRID:AB_2574616 | “1:20” |
| Antibody | anti-CD3 -biotin (Mouse monoclonal) | Biolegend | BioLegend Cat# 317320, RRID:AB_10916519 | 3.2µl/10x107 cells |
| Antibody | anti-CD14 biotin (Mouse monoclonal) | Biolegend | BioLegend Cat# 367105, RRID:AB_2566617 | 4.8µl/10x107 |
| Antibody | anti-CD19 -biotin (Mouse monoclonal) | Biolegend | BioLegend Cat# 302204, RRID:AB_314234 | 4.8µl/10x107 |
| Antibody | anti-CD66b-biotin (Mouse monoclonal) | Biolegend | ioLegend Cat# 305120, RRID:AB_2566608 | 2.4µl/10x107 |
| Antibody | anti-CD8a -BV510(Mouse monoclonal) | Biolegend | BioLegend Cat# 301048, RRID:AB_2561942 | “1:50” |
| Antibodx | anti-CD4-APC (Mouse monoclonal) | Biolegend | BioLegend Cat# 317416, RRID:AB_571945 | “1:100” |
| Antibody | anti-CD3delta -R-PE (Mouse monoclonal) | lifetechnologies | Thermo Fisher Scientific Cat# MHCD0304, RRID:AB_10376004 | “1:50” |
| Antibody | anti-CD2-APC (Mouse monoclonal) | Biolegend | BioLegend Cat# 300214, RRID:AB_10895925 | “1:100” |
| Commercial assay or kit | Foxp3 staining kit | ThermoFisher | Cat: 00-5523-00 | |
| Commercial assay or kit | Fixation buffer | Biolegend | Cat: 420801 | |
| Commercial assay or kit | LEGENDplex | Biolegend | Cat: 740722 |
Human T Helper Cytokine Panel |
| Commercial assay or kit | MojoSortStreptavidin Nanobeads | Biolegend | Cat: 480016 | 50µl/10x107 |
| Commercial assay or kit | Illumina Tagment DNA Enzyme and Buffer Small Kit |
Illumina | Cat: 15027865 | TDE1 enzyme |
| Software, algorithm | Kaluza 2.1 | Beckman Coulter | Kaluza, RRID:SCR_016182 | Version 2.1 |
| Software, algorithm | t-SNE embedded in FlowJo | BD Bioscience | FlowJo, RRID:SCR_008520 | 500 iterations for the t-SNE calculations |
| Software, algorithm | ENCODE-ATACseq-pipeline | https://github.com/kundajelab/atac_dnase_pipelines | ||
| Software, algorithm | cutadapt | Martin, 2011 | cutadapt, RRID:SCR_011841 | Version 2.3 |
| Software, algorithm | Bowtie2 | Langmead and Salzberg, 2012 | Version 2.3.4 | |
| Software, algorithm | PICARD | http://broadinstitute.github.io/picard/ | Picard, RRID:SCR_006525 | Version 2.20.2 |
| Software, algorithm | SAMtools | Li et al., 2009 | SAMTOOLS, RRID:SCR_002105 | Version 1.9 |
| Software, algorithm | Deeptools bamCoverage |
Ramírez et al., 2016 | Deeptools, RRID:SCR_016366 | |
| Software, algorithm | Macs2 | Zhang et al., 2008 | ||
| Software, algorithm | R package DESeq2 | Love et al., 2014 | DESeq2, RRID:SCR_015687 | Version 1.22.2 |
| Software, algorithm | R package vidger | MacDermaid et al 2018 | Version 1.2.1 | |
| Software, algorithm | GraphPad Prism | www.graphpad.com | GraphPad Prism, RRID:SCR_002798 | Version 8.0.0 |