ab _ 2814142 totalseq - a0868 anti-human ige ( mhe - 18 ) biolegend 325517; rrid: ab _ 2814186 totalseq - a0869 anti-human cd365 ( 1d12 ) biolegend 353907; rrid: ab _ 2814294 totalseq - a0870 anti-human cd150 ( a12 ) biolegend 306313; rrid: ab _ 2814146 totalseq - a0871 anti-human cd162 ( kpl - 1 ) biolegend 328821; rrid: ab _ 2814192 totalseq - a0875 anti-mouse tlr4 ( mts510 ) biolegend 117614; rrid: ab _ 2810352 totalseq - a0876 anti-mouse cd300c _ d ( tx52 ) biolegend 148005; rrid: ab _ 2810413 totalseq - a0877 anti-mouse jaml ( 4e + 10 ) biolegend 128507; rrid: ab _ 2810391 totalseq - a0881 anti-mouse cd272 ( 6a6 ) biolegend 139113; rrid: ab _ 2814041 totalseq - a0882 anti-mouse pira _ pirb ( 6c1 ) biolegend 144105; rrid: ab _ 2810412 totalseq - a0883 anti-mouse cd26 ( h194 - 112 ) biolegend 137811; rrid: ab _ 2810405 totalseq - a0884 anti-mouse dll1 ( hmd1 - 3 ) biolegend 128315; rrid: ab _ 2810390 totalseq - a0885 anti-mouse cd270 ( hmhc - 1b18 ) biolegend 136307; rrid: ab _ 2810403 totalseq - a0890 anti-mouse 4 _ 1bb ( tks - 1 ) biolegend 107109: rrid: ab _ 2813955 totalseq - a0891 anti-mouse enpp ( ye1 / 19. 1 ) biolegend 149209; rrid: ab _ 2814052 totalseq - a0892 anti-mouse cd2 ( rm2 - 5 ) biolegend 100117; rrid: ab _ 2810312 totalseq - a0894 anti-human ig ( mhl - 38 ) biolegend 316531; rrid: ab _ 2810479 totalseq - a0895 anti-mouse / human mac2 ( lm3 / 38 ) biolegend 125421; rrid: ab _ 281384 totalseq - a0896 anti-human cd85j ( ghi / 75 ) biolegend 333723; rrid: ab _ 2814225 totalseq - a0897 anti-human cd23 ( ebvcs - 5 ) biolegend 338523; rrid: ab _ 2814235 totalseq - a0898 anti-human ig ( mhk - 49 ) biolegend 316627; rrid: ab _ 2814170 totalseq - a0899 anti-human hla - a2 ( bb7. 2 ) biolegend 343331; rrid: ab _ 2810540 totalseq - a0900 anti-human cd198 ( l263g8 ) biolegend 360607; rrid: ab _ 2810572 totalseq - a0901 anti-human garp ( 7b11 ) biolegend 352515; rrid: ab _ 2814283 totalseq - a0904 anti-mouse cd31 ( 390 ) biolegend 102437; rrid: ab _ 2810335 totalseq - a0905 anti-mouse cd107a ( 1d4b ) biolegend 121635; rrid: ab _ 2810369 totalseq - a0916 anti-mouse cd124 ( i015f8 ) biolegend 144809; rrid: ab _ 2814050 totalseq - a0917 anti-mouse cd95 ( sa367h8 ) biolegend 152614; rrid: ab _ 2810418 totalseq - a0923 anti-human nkp80 ( 5d12 ) biolegend 346709; rrid: ab _ 2814274 totalseq - a5106 anti-mouse ly6d biolegend barcode: atgtcctacctcaaa chemicals, peptides, and recombinant p roteins antigenfix diapath p0014 β - mercaptoethanol sigma - aldrich m3148 calcium chloride dih ydrate merck 1023821000 collagenase a sigma - aldrich 11088793001 d - ( - ) - fructose merck - millipore 1040071000 d ( + ) - saccharose vwr international prol27483. 294 dapi invitrogen d1306; ridd: ab _ 2629482 dmem invitrogen 41965 - 039 dnase i sigma - aldrich 04 536 282 001 donkey serum abcam ab7475 edta westburg 51234 egta sigma - aldrich e3889 eosin vwr international merc 1. 15935 fcblock 2. 4g2 bioceros n / a fcs bodinco 5010 fixable viability due live / dead - efluor506 ebioscience 65 - 0866 - 18 fixable viability due live / dead - efluor780 ebioscience 65 - 0865 - 18 fixation / permeabilization solution kit bd cytofix / cytoperm 554714 foxp3 transcription factor staining buffer kit ebioscience 00 - 5523 - 00 gentamicin gibco 15710 - 049 glutamax thermo fisher 35050 - 038 gluteraldehyde 25 % sigma - aldrich g5882 goat serum sigma - aldrich g9023 hematoxylin vwr international merc1. 05174 hepes sigma - aldrich h3375 iso propanol vel t0108 methanol merck millipore 13680502 paraformaldehyde 10 % ems 15712 phenol red sigma - aldrich p3532 prolong diamond thermo fisher p36970 rat serum sigma - aldrich r9759 ribonucleoside vanadyl complexes sigma - aldrich r3380 - 5ml roche protector rnase inhibitor sigma - aldrich 3335399001 rpmi 1640 gibco 52400 - 025 saponin sigma - aldrich 4521 10x sds sigma - aldrich 71736 - 100ml sodium bicarbonate sigma - aldrich 792519 sodium chloride sigma - aldrich 746398 sodium dih ydrogen phosphate monohydrate sigma - aldrich 1063461000 sodium phosphate dibasic dih ydrate sigma - aldrich 71643 tissue - tek o. c. t sakura finetek 4583 ultrapure™ salmon sperm dna solution thermo fisher scientific 15632011 xylene prolabo prol28973. 363 critical commercial assays allin hs red taq mastermix 2x highqu hq. hsm0350 rneasy plus micro kit qiagen 74034 sensifast cdna synthesis kit bioline bio - 65054 sensifast sybr no - rox kit bioline bio - 98020 visium spatial gene expression slide and reagent kit 10x genomics 1000184 oligo nucleot ides: qpcr flt3 – qpcr fwd idt gtgactggccccctggataacgag flt3 – qpcr rev idt tccaagggcgggtgtaactgaact xcr1 - qpcr fwd idt agagacaccgaacagtcaggct xcr1 - qpcr rev idt tgtccagttgctgaaggctctc cd209a - qpcr fwd idt gcactccatcaaaggctttggc cd209a - qpcr rev idt caaacagctaggaagagcacctg ccr7 - qpcr fwd idt agaggctcaagaccatgacgga ccr7 - qpcr rev idt tccaggacttggcttcgctgta mafb - qpcr fwd idt tgaatttgctggcactgctg mafb - qpcr rev idt aagcaccatgcggttcataca cd5l - qpcr fwd idt gaggacacatggatggaatgt cd5l - qpcr rev idt acccttgtgtagcacctcca cd207 - qpcr fwd idt ccgaagcgcacttcacagt cd207 - qpcr rev idt gcagatacagagaggtttcctca spp1 - qpcr fwd idt ccatctcagaagcagaatctcctt spp1 - qpcr rev idt ggtcatggctttcattggaatt gata6 - qpcr fwd idt cagcaggacccttcgaaac gata6 - qpcr rev idt ccattcatcttgctgtagagacc gpnmb - qpcr fwd idt agcacaaccaattacgtggc gpnmb - qpcr rev idt cttcccaggagtccttcca pla2g7 - qpcr fwd idt cttcaagcccttagtgaggacc pla2g7 - qpcr rev idt tgcgatgtcctttggagtctgg cd9 - qpcr fwd idt gctactcgagccatgccggtca aaggaggtagc cd9 - qpcr rev idt cacttggtaccgaccatttctc ggctcctgcg cd36 - qpcr fwd idt ggagccatctttgagccttca cd36 - qpcr rev idt gaaccaaactgaggaatggatct il1b - qpcr fwd idt gcaactgttcctgaactcaact il1b - qpcr rev idt atcttttggggtccgtcaact tnf - qpcr fwd idt tcttctcattcctgcttgtgg tnf - qpcr rev idt ggtctgggccatagaactga il10 - qpcr fwd idt aaggcagtggagcaggtgaa il10 - qpcr rev idt ccagcagactcaatacacac il18 - qpcr fwd idt actgtacaaccgcagtaatacgc il18 - qpcr rev idt agtgaacattacagatttatccc actb - qpcr fwd idt gcttctaggcggactgttactga actb - qpcr rev idt gccatgccaatgttgtctcttat oligo nucleot ides: molecular cartography probes flt3 resolve bio. pzm6j software and algorithms adobe illustrator adobe www. adobe. com cell ranger 10x genomics https: / / support. 10xgenomics. com / single - cell - gene - expression / software / pipelines / latest / what - is - cell - ranger fastcar r package n / a https: / / github. com / lungcellatlas / fastcar seurat r package v3 ( stuart et al., 2019 ) https: / / satijalab. org / seurat / scater r package ( mccarthy et al., 2017 ) https: / / bioconductor. org / packages / release / bioc / html / scater. html biomart n / a https: / / www. ensembl. org / biomart / martview / 3e2c65a5e3f783f8c9e5d648e4b64126 pheatmap r package n / a https: / / rdrr. io / cran / pheatmap / ggplot2 ( wickham 2016 ) https: / / ggplot2. tidyverse. org scanpy ( wolf et al., 2018 ) https: / / scanpy. readthedocs. io / en / stable / pytorch n / a https: / / pytorch. org totalvi ( gayoso et al., 2021 ) https: / / docs. scvi - tools. org / en / stable / user _ guide / models / totalvi. html scvi ( lopez et al., 2018 ) https: / / docs. scvi - tools. org / en / stable / user _ guide / models / totalvi. html nichenet ( browaeys et al. 2019 ) https: / / github. com / saeyslab / nichenetr enrichr ( kuleshov et al., 2016 ) http: / / amp. pharm. mssm. edu / enrichr / flowjo v10. 6. 1 flowjo https: / / www. flowjo. com geneontology ( ashburner et al., 2000 ) http: / / geneontology. org / graphpad prism 9 graphpad https: / / www. graphpad. com / harmony ( korsunsky et al., 2019 ) https: / / www. github. com / immunogenomics / harmony ilastik ( berg et al., 2019 ) https: / / www. ilastik. org / imagej ( schneider et al., 2012 ) https: / / imagej. nih. gov / ij qi - tissue