KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| EPCAM/CD326, clone 9C4, Mouse IgG2b | Biolegend | Cat# 324233 |
| CD45, clone HI30, mouse IgG1 | Biolegend | Cat# 304005 |
| CD31, clone WM59, mouse IgG1 | Biolegend | Cat# 303133 |
| CD146, clone P1H12, Mouse IgG1 | Biolegend | Cat# 361003 |
| PDPN, clone NZ-1.3, rat IgG2a | eBioscience/ThermoFisher | Cat #46-4321-82 |
| CD90, clone 5E10, mouse IgG1 | Biolegend | Cat# 328109 |
| Alexa Fluor® 647 - Mouse monoclonal (D2-40) anti-Podoplanin (Lymphatic Endothelial Marker) antibody | Biolegend | Cat# 916610 RRID : AB_2810816 |
| BSA and Azide free -Recombinant Rabbit monoclonal [EPR5480] Anti PDGFR alpha | Abcam | Cat# ab248689 RRID : N/A |
| Alexa Fluor® 488 - Recombinant Rabbit monoclonal [EPR3208] Anti-CD146 antibody | Abcam | Cat# ab196448; RRID:AB_2868591 |
| BSA and Azide free – Recombinant Rabbit monoclonal [EPR3132] Anti CD90 / Thy1 antibody | Abcam | Cat# ab181885 RRID : N/A |
| Alexa Fluor® 555 – Recombinant Rabbit monoclonal [EPR20545] Anti-CD68 antibody | Abcam | Cat# ab280860 RRID : N/A |
| BSA and Azide free - Recombinant Rabbit monoclonal [SP162] Anti-CD3 antibody | Abcam | Cat# ab245731 RRID : N/A |
| Alexa Fluor® 647 – Mouse monoclonal (JC/70A) anti CD31/PECAM-1 antibody | Novus | Cat# NB600-562AF647 RRID: N/A |
| Alexa Fluor® 647 – Mouse monoclonal (C31.3) anti CD31/PECAM-1 antibody | Novus | Cat# NB P2-33154AF647 RRID: N/A |
| BSA and Azide free – Recombinant Rabbit monoclonal [SP205] Anti-SPARC antibody | Abcam | Cat# ab245733 RRID: N/A |
| Unconjugated - Goat Polyclonal Anti-Human Ccl19 / mip-3 beta antibody | R and D systems | Cat# AF361; RRID:AB_355323 |
| Alexa Fluor® 488 – Mouse monoclonal [1A4] Anti-alpha smooth muscle Actin antibody | Abcam | Cat# ab184675; RRID:AB_2832195 |
| Alexa Fluor® 647 Mouse monoclonal (2D1) anti-human CD45 antibody | BioLegend | Cat# 368538; RRID:AB_2716028 |
| Alexa Fluor® 647 Mouse monoclonal (C8/144B) anti-human CD8a antibody | BioLegend | Cat# 372906; RRID:AB_2650712 |
| Alexa Fluor® 488 Recombinant Rabbit monoclonal [EP1628Y] Anti-Cytokeratin 8 antibody | Abcam | Cat# ab192467; RRID:AB_2864346 |
| Alexa Fluor® 555 Recombinant Rabbit monoclonal [EPR3776] Anti-Vimentin antibody - Cytoskeleton Marker | Abcam | Cat# ab203428 RRID : N/A |
| Alexa Fluor® 488 Mouse monoclonal (TAL 1B5) Anti-HLA-DR Antibody | Santacruz | Cat# sc-53319AF488 RRID N/A |
| Donkey anti-Goat IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 | Thermo Fisher Scientific | Cat# A-21447; RRID:AB_2535864 |
| Donkey anti-Rabbit IgG (H + L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555 | Thermo Fisher Scientific | Cat# A-31572; RRID:AB_162543 |
| CD16/CD32 Monoclonal Antibody (93) (FcR block) 1:200 | ThermoFisher Scientific | 14-0161-86 |
| FITC EpCAM (G8.8) 1:200 | Biolegend | 118208 |
| PE-Cy7 Podoplanin (8.1.1) 1:200 | Biolegend | 127412 |
| APC CD140a (APA5)1:200 | Biolegend | 135907 |
| BV605 CD31 (390) 1:200 | Biolegend | 102427 |
| BV711 CD45 (30-F11) 1:200 | Biolegend | 103147 |
| BV711 CD45 (30-F11) 1:200 | Biolegend | 103147 |
| Bacterial and virus strains | ||
| Mycobacterium tuberculosis H37Ra | BD Difco | BD 231141 |
| Chemicals, peptides, and recombinant proteins | ||
| Glycerol | Sigma-Aldrich | Cat# G5516 RRID N/A |
| Trizma®base | Sigma-Aldrich | Cat# T6066 RRID N/A |
| Sodium bicarbonate | Sigma-Aldrich | Cat#S6297 RRID N/A |
| Tween20 | Sigma-Aldrich | Cat#P9416 RRID N/A |
| Triton X-100 | Sigma-Aldrich | Cat#T9284 RRID N/A |
| Propyl gallate | Sigma-Aldrich | Cat#02370 RRID N/A |
| Bovine Serum Albumin | Sigma-Aldrich | Cat#A7906 RRID N/A |
| Target Retrieval Solution 10X Concentrate | Dako | Cat#S1699 |
| Ethylenediaminetetraacetic acid | Sigma-Aldrich | Cat#E9884 |
| eBioscience Fixable Viability Dye eFluor 780 1:1000 | ThermoFisher Scientific | 65-0865-18 |
| DAPI Solution 50 pg/mL | ThermoFisher Scientific | 62248 |
| 2.5% w/v dextran sulfate sodium | MP Biomedicals | 216011080 |
| Liberase TL | Roche | 5401020001 |
| DNase 1 | Sigma | 11284932001 |
| Quick-RNA 96 Kit | Zymo Research | R1052 |
| Donkey Serum | Biorad | Cat# C06SB RRID N/A |
| Hydrogen Peroxide Solution | Sigma-Aldrich | Cat#216763 RRID N/A |
| FcR Blocking Reagent | Miltenyi | Cat# 130-059-901; RRID:AB_2892112 |
| Bovine Tyope II Collagen | Richard Williams https://doi.org/10.1385/1-59259-771-8:207 |
N/A |
| Critical commercial assays | ||
| Dynabeads Human T-activator CD3/CE28 for T cell expansion and activation | ThermoFisher | Cat# 11132D |
| 10× Genomics Chromium Single Cell 3’ (v2 and v3 chemistry) | 10× Genomics | https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/technical-note-assay-scheme-and-configuration-of-chromium-single-cell-3-v2-libraries |
| Cell Dive | General Electric | https://www.ge.com/research/project/multiplexed-tissue-imaging-platform |
| CD45RA MicroBeads (human) | Miltenyi | Cat# 130-045-901 |
| Pan T Cell Isolation Kit (human) | Miltenyi | Cat# 130-096-535 |
| LS columns | Miltenyi | Cat# 130-042-401 |
| Deposited data | ||
| CellDive imaging data: https://www.immport.org/shared/study/SDY1765 | This paper | ImmPort:SDY1765 |
| Human fibroblast atlas: https://sandbox.zenodo.org/record/772596#.YGsi6BRKg-Q | This paper | https://doi.org/10.5072/zenodo.772596 |
| Atopic dermatitis scRNAseq | He et al., 2020a | GSE147424 |
| Serum transfer arthritis scRNAseq | Wei et al., 2020 | GSE145286 |
| DSS induced colitis scRNAseq | Kinchen et al., 2018 | GSE114374 |
| bleomycin induced lung injury scRNAseq | Tsukui et al., 2020 | GSE132771 |
| Adult human cell atlas | He et al., 2020b | GSE159929 |
| Tabula sapiens: https://figshare.com/projects/Tabula_Sapiens/100973 | The Tabula Sapiens Consortium and Quake, 2021 | N/A |
| Healthy lung atlas scRNAseq | Travaglini et al. | Synapse:syn21041850 |
| IPF lung cohort scRNAseq | Adams et al. | GSE136831 |
| Healthy gut atlas scRNAseq | Elmentaite et al., 2021 | E-MTAB-9536 |
| Raw human sequencing data: https://www.immport.org/shared/study/SDY1765 | This paper | ImmPort:SDY1765 |
| Processed human sequencing data:https://singlecell.broadinstitute.org/single_cell/study/SCP738 | This paper | BroadSingleCellPortal:SCP738 |
| Raw and processed mouse sequencing data | This paper | GSE185711 |
| Experimental models: Cell lines | ||
| Primary lung fibroblast cell lines from earlier-stage fibrotic interstitial lung disease | This paper | Lung fibroblast cell lines named V3, V6, V7, V11. |
| Primary Synovial fibroblasts | This paper | synovial fibroblast cell lines named: STB-009, RA200212, AMP-005 |
| Primary human T cells isolated from leukopak mononuclear cells | This paper | N/A |
| Collagen Induced Arthritis | https://doi.org/10.1385/1-59259-771-8:207 | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | Jackson Laboratory | RRID:IMSR_JAX:000,664 |
| Mouse: DBA/1J | MRC Harwell | N/A |
| Software and algorithms | ||
| Code to Reproduce Analyses and Figures for Fibroblast Atlas 2022 | This Paper | https://doi.org/10.5281/zenodo.6510339 |
| Symphony v1.0 | Kang et al., 2021 | https://github.com/immunogenomics/symphony |
| DeepCell | Greenwald et al., 2021 | https://github.com/vanvalenlab/deepcell-tf |
| uwot v0.1.10 | Melville et al., 202068 | https://github.com/jlmelville/uwot |
| arm v1.11.2 | Gelman and Su, 202093 | https://github.com/gelman/arm |
| lme4 v1.1.27.1 | Bates et al., 2015 | https://github.com/lme4/lme4 |
| presto | This paper | https://github.com/immunogenomics/presto/tree/glmm |
| fgsea v1.18.0 | Sergushichev, 2016 | https://github.com/ctlab/fgsea |
| msigdbr v7.4.1 | Dolgalev, 201894 | https://github.com/igordot/msigdbr |
| scanorama v1.7.1 | Hie et al., 2019 | https://github.com/brianhie/scanorama |
| bbknn v1.5.1 | Polański et al., 2020 | https://github.com/Teichlab/bbknn |
| scvi-tools v0.6.8 | Lopez et al., 2018 | https://github.com/scverse/scvi-tools |
| scanpy v1.7.1 | Wolf et al., 2018 | https://github.com/scverse/scanpy |
| VGAM v1.1.5 | Yee, 2010 | https://github.com/cran/VGAM |
| limma v3.48.3 | Ritchie et al., 2015 | https://github.com/cran/limma |
| kallisto | Bray et al., 2016 | https://github.com/pachterlab/kallisto |
| bustools | Melsted et al., 2019 | https://github.com/BUStools/bustools |
| harmony v1.0 | Korsunsky et al., 2019 | https://github.com/immunogenomics/harmony/tree/weights |