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cell idtm 20 plex pd barcoding kit fluidigm  (fluidigm)


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    fluidigm cell idtm 20 plex pd barcoding kit fluidigm
    Cell Idtm 20 Plex Pd Barcoding Kit Fluidigm, supplied by fluidigm, used in various techniques. Bioz Stars score: 96/100, based on 650 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cell+idtm+20+plex+pd+barcoding+kit+fluidigm/Cell-ID+20-Plex+Pd+Barcoding+Kit/10__7554_slash_elife__99323__3-613-54-61
    Average 96 stars, based on 650 article reviews
    cell idtm 20 plex pd barcoding kit fluidigm - by Bioz Stars, 2026-09
    96/100 stars

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    Red Blood Cell Lysis:

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors
    Article Snippet: Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 ..

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Vimentin (D21H3) XP Rabbit Cell Signaling Technology Cat# 5741S; RRID: AB_10695459 Histone H3 (D1H2) XP Cell Signaling Technology Cat# 4499S; RRID: AB_10544537 Histone H3 Phospho (Ser28) BioLegend Cat# 641002; RRID: AB_1227659 Mitochondria Abcam Cat# ab92824; RRID: AB_10562769 Ki-67 Cell Signaling Technology Cat# 9449; RRID: AB_2797703 a-Smooth Muscle Actin Cell Signaling Technology Cat# 19245; RRID: AB_2734735 CD31 Abcam Cat# ab225883 Citrate Synthase Abcam Cat# ab129095 GLUT1 Abcam Cat# ab115730; RRID: AB_2832207 H2AX (pS139), gH2AX BD Biosciences Cat# 560443; RRID: AB_1645592 Synaptophysin Novus Cat# NBP1-47483; RRID: AB_10010435 H3K27ac Thermo Fisher Scientific Cat# MA5-23516; RRID: AB_2608307 H3K4me2 Thermo Fisher Scientific Cat# 701764; RRID: AB_2532505 H4K8ac Thermo Fisher Scientific Cat# 701796; RRID: AB_2532510 mCherry Abcam Cat# ab167453; RRID: AB_2571870 GFP Abcam Cat# ab183735; RRID: AB_2732027 VSV-G Tag Thermo Fisher Scientific Cat# PA1-30138; RRID: AB_1961360 E2 Tag GenScript Cat# A00630; RRID: AB_914515 Strep Tag II GenScript Cat# A01732; RRID: AB_2622218 Protein C Tag GenScript Cat# A01774; RRID: AB_2744686 Tag-100 Tag GenScript Cat# A00677; RRID: AB_915550 AU1 Tag Bethyl Cat# A190-124A; RRID: AB_155848 FLAG Tag Millipore-Sigma Cat# F1804; RRID: AB_262044 HA Tag Thermo Fisher Scientific Cat# 26183; RRID: AB_10978021 Cleaved caspase 3 BD Biosciences Cat# 559565; RRID: AB_397274 NEUROD1 Abcam Cat# ab109224; RRID: AB_10861489 YAP1 Cell Signaling Technology Cat# 14074; RRID: AB_2650491 NOTCH2 Cell Signaling Technology Cat#5732; RRID: AB_10693319 Hexokinase-1 Abcam Cat# ab150423; RRID: N/A H4K12ac Thermo Fisher Scientific Cat# 712991; RRID: AB_2895909 Na+ K+ ATPase Abcam Cat# ab167390; RRID: AB_2890241 H3K4me1 Thermo Fisher Scientific Cat# 710795; RRID: AB_2532764 ATP5A Abcam Cat# ab14748; RRID: AB_301447 CD56 Ionpath Cat# 715101-100; RRID: AB_2861293 H4K20me1 Thermo Fisher Scientific Cat# MA5-18067; RRID: AB_2539450 SLC1A5 / ASCT2 Abcam Cat# ab251591; RRID: N/A CD107a (LAMP-1) BioLegend Cat# 328602; RRID: AB_1134259 H3K9ac Cell Signaling Technology Cat# 9649; RRID: AB_823528 H3K27me3 Cell Signaling Technology Cat# 9733; RRID: AB_2616029 ImmPRESS HRP Horse anti-Rabbit IgG Vector Labs MP-7801-15 Alexa Fluor 594 Donkey anti-Goat IgG Thermo Fisher Scientific Cat# A-11058; RRID: AB_2534105 Alexa Fluor 488 Donkey anti-Rabbit IgG Thermo Fisher Scientific Cat# A-21206, RRID: AB_2535792 Bacterial and virus strains Endura Chemically Competent Cells Lucigen Cat# 60240-1 (Continued on next page) e1 Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2

    Immunohistochemistry:

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors
    Article Snippet: Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 ..

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Vimentin (D21H3) XP Rabbit Cell Signaling Technology Cat# 5741S; RRID: AB_10695459 Histone H3 (D1H2) XP Cell Signaling Technology Cat# 4499S; RRID: AB_10544537 Histone H3 Phospho (Ser28) BioLegend Cat# 641002; RRID: AB_1227659 Mitochondria Abcam Cat# ab92824; RRID: AB_10562769 Ki-67 Cell Signaling Technology Cat# 9449; RRID: AB_2797703 a-Smooth Muscle Actin Cell Signaling Technology Cat# 19245; RRID: AB_2734735 CD31 Abcam Cat# ab225883 Citrate Synthase Abcam Cat# ab129095 GLUT1 Abcam Cat# ab115730; RRID: AB_2832207 H2AX (pS139), gH2AX BD Biosciences Cat# 560443; RRID: AB_1645592 Synaptophysin Novus Cat# NBP1-47483; RRID: AB_10010435 H3K27ac Thermo Fisher Scientific Cat# MA5-23516; RRID: AB_2608307 H3K4me2 Thermo Fisher Scientific Cat# 701764; RRID: AB_2532505 H4K8ac Thermo Fisher Scientific Cat# 701796; RRID: AB_2532510 mCherry Abcam Cat# ab167453; RRID: AB_2571870 GFP Abcam Cat# ab183735; RRID: AB_2732027 VSV-G Tag Thermo Fisher Scientific Cat# PA1-30138; RRID: AB_1961360 E2 Tag GenScript Cat# A00630; RRID: AB_914515 Strep Tag II GenScript Cat# A01732; RRID: AB_2622218 Protein C Tag GenScript Cat# A01774; RRID: AB_2744686 Tag-100 Tag GenScript Cat# A00677; RRID: AB_915550 AU1 Tag Bethyl Cat# A190-124A; RRID: AB_155848 FLAG Tag Millipore-Sigma Cat# F1804; RRID: AB_262044 HA Tag Thermo Fisher Scientific Cat# 26183; RRID: AB_10978021 Cleaved caspase 3 BD Biosciences Cat# 559565; RRID: AB_397274 NEUROD1 Abcam Cat# ab109224; RRID: AB_10861489 YAP1 Cell Signaling Technology Cat# 14074; RRID: AB_2650491 NOTCH2 Cell Signaling Technology Cat#5732; RRID: AB_10693319 Hexokinase-1 Abcam Cat# ab150423; RRID: N/A H4K12ac Thermo Fisher Scientific Cat# 712991; RRID: AB_2895909 Na+ K+ ATPase Abcam Cat# ab167390; RRID: AB_2890241 H3K4me1 Thermo Fisher Scientific Cat# 710795; RRID: AB_2532764 ATP5A Abcam Cat# ab14748; RRID: AB_301447 CD56 Ionpath Cat# 715101-100; RRID: AB_2861293 H4K20me1 Thermo Fisher Scientific Cat# MA5-18067; RRID: AB_2539450 SLC1A5 / ASCT2 Abcam Cat# ab251591; RRID: N/A CD107a (LAMP-1) BioLegend Cat# 328602; RRID: AB_1134259 H3K9ac Cell Signaling Technology Cat# 9649; RRID: AB_823528 H3K27me3 Cell Signaling Technology Cat# 9733; RRID: AB_2616029 ImmPRESS HRP Horse anti-Rabbit IgG Vector Labs MP-7801-15 Alexa Fluor 594 Donkey anti-Goat IgG Thermo Fisher Scientific Cat# A-11058; RRID: AB_2534105 Alexa Fluor 488 Donkey anti-Rabbit IgG Thermo Fisher Scientific Cat# A-21206, RRID: AB_2535792 Bacterial and virus strains Endura Chemically Competent Cells Lucigen Cat# 60240-1 (Continued on next page) e1 Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2

    Electron Microscopy:

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors
    Article Snippet: Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 ..

    Article Title: Spatial epitope barcoding reveals clonal tumor patch behaviors.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Vimentin (D21H3) XP Rabbit Cell Signaling Technology Cat# 5741S; RRID: AB_10695459 Histone H3 (D1H2) XP Cell Signaling Technology Cat# 4499S; RRID: AB_10544537 Histone H3 Phospho (Ser28) BioLegend Cat# 641002; RRID: AB_1227659 Mitochondria Abcam Cat# ab92824; RRID: AB_10562769 Ki-67 Cell Signaling Technology Cat# 9449; RRID: AB_2797703 a-Smooth Muscle Actin Cell Signaling Technology Cat# 19245; RRID: AB_2734735 CD31 Abcam Cat# ab225883 Citrate Synthase Abcam Cat# ab129095 GLUT1 Abcam Cat# ab115730; RRID: AB_2832207 H2AX (pS139), gH2AX BD Biosciences Cat# 560443; RRID: AB_1645592 Synaptophysin Novus Cat# NBP1-47483; RRID: AB_10010435 H3K27ac Thermo Fisher Scientific Cat# MA5-23516; RRID: AB_2608307 H3K4me2 Thermo Fisher Scientific Cat# 701764; RRID: AB_2532505 H4K8ac Thermo Fisher Scientific Cat# 701796; RRID: AB_2532510 mCherry Abcam Cat# ab167453; RRID: AB_2571870 GFP Abcam Cat# ab183735; RRID: AB_2732027 VSV-G Tag Thermo Fisher Scientific Cat# PA1-30138; RRID: AB_1961360 E2 Tag GenScript Cat# A00630; RRID: AB_914515 Strep Tag II GenScript Cat# A01732; RRID: AB_2622218 Protein C Tag GenScript Cat# A01774; RRID: AB_2744686 Tag-100 Tag GenScript Cat# A00677; RRID: AB_915550 AU1 Tag Bethyl Cat# A190-124A; RRID: AB_155848 FLAG Tag Millipore-Sigma Cat# F1804; RRID: AB_262044 HA Tag Thermo Fisher Scientific Cat# 26183; RRID: AB_10978021 Cleaved caspase 3 BD Biosciences Cat# 559565; RRID: AB_397274 NEUROD1 Abcam Cat# ab109224; RRID: AB_10861489 YAP1 Cell Signaling Technology Cat# 14074; RRID: AB_2650491 NOTCH2 Cell Signaling Technology Cat#5732; RRID: AB_10693319 Hexokinase-1 Abcam Cat# ab150423; RRID: N/A H4K12ac Thermo Fisher Scientific Cat# 712991; RRID: AB_2895909 Na+ K+ ATPase Abcam Cat# ab167390; RRID: AB_2890241 H3K4me1 Thermo Fisher Scientific Cat# 710795; RRID: AB_2532764 ATP5A Abcam Cat# ab14748; RRID: AB_301447 CD56 Ionpath Cat# 715101-100; RRID: AB_2861293 H4K20me1 Thermo Fisher Scientific Cat# MA5-18067; RRID: AB_2539450 SLC1A5 / ASCT2 Abcam Cat# ab251591; RRID: N/A CD107a (LAMP-1) BioLegend Cat# 328602; RRID: AB_1134259 H3K9ac Cell Signaling Technology Cat# 9649; RRID: AB_823528 H3K27me3 Cell Signaling Technology Cat# 9733; RRID: AB_2616029 ImmPRESS HRP Horse anti-Rabbit IgG Vector Labs MP-7801-15 Alexa Fluor 594 Donkey anti-Goat IgG Thermo Fisher Scientific Cat# A-11058; RRID: AB_2534105 Alexa Fluor 488 Donkey anti-Rabbit IgG Thermo Fisher Scientific Cat# A-21206, RRID: AB_2535792 Bacterial and virus strains Endura Chemically Competent Cells Lucigen Cat# 60240-1 (Continued on next page) e1 Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2 .. Cas9 Integrated DNA Technologies Cat# 1081059 Polyethylenimine (PEI) Polysciences Cat# 23966-1 Polybrene Millipore-Sigma Cat# TR-1003-G Opti-MEM Thermo Fisher Scientific Cat# 31985088 RPMI 1640 Corning Cat# 15-040-CV DMEM Thermo Fisher Scientific Cat# 11965092 Bovine Growth Serum Thermo Fisher Scientific Cat# SH3054103HI Penicillin-Streptomycin-Glutamine Thermo Fisher Scientific Cat# 10378016 Fetal Bovine Serum Thermo Fisher Scientific Cat#16000044 Matrigel BD biosciences Cat# 356237 Tris(2-carboxyethyl) phosphine hydrochloride (TCEP) Thermo Fisher Scientific Cat# 77720 PBS antibody stabilizer Thermo Fisher Scientific Cat# NC0414486 Paraformaldehyde (PFA) Thermo Fisher Scientific Cat# 28906 Saponin Millipore-Sigma Cat# S7900-100G Bovine Serum Albumin (BSA) Millipore-Sigma Cat# A3059 Sodium azide Millipore-Sigma Cat# 71289 Cell-ID Intercalator-Ir Fluidigm Cat# 201192B L15 media Millipore-Sigma Cat# L1518 Collagenase I Millipore-Sigma Cat# C0130 Collagenase II Millipore-Sigma Cat# 6885 Collagenase IV Millipore-Sigma Cat# 5138 Elastase CellSystems Cat# LS002292 DNAseI Millipore-Sigma Cat# 10104159 RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 Histogel Thermo Fisher Scientific Cat# NC9150318 Vectabond Vector Labs Cat# SP-1800-7 1X Dako Target Retrieval Solution Agilent Cat# S2375 1X TBS IHC wash buffer with Tween 20 Cell Marque Cat# 935B-09 Donkey serum Millipore-Sigma Cat# D9663-10ML Triton X-100 Millipore-Sigma Cat# T8787-100ML Glutaraldehyde Electron Microscopy Sciences Cat# 16120 H-3300 Vector Labs Cat# H-3300-250 DAB reagent Vector Labs Cat# SK-4100 Hematoxylin Millipore-Sigma Cat# HHS32 Refrax Mounting Medium Anatech Ltd Cat# 711 Fluoromount-G SouthernBiotech Cat# 0100-01 Histo-Clear II National Diagnostics Cat# HS-202 Hydrogen peroxide VWR Cat# BP2633-500 Horse serum Thermo Fisher Cat# 16050-130 Critical commercial assays SE Cell Line 4D-NucleofectorTM X Kit S Lonza Cat# V4XC-1032 Herculase II Fusion DNA Polymerase kit Agilent Cat# 600675 Maxpar X8 polymers Fluidigm Cat# 201300 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 TSA Plus Fluorescein kit Akoya Biosciences Cat# NEL741001KT Deposited data Source data for datasets 1 to 3 and the code for debarcoding Mendeley Data https://data.mendeley.com/datasets/ 4y3fzctgxn/draft?a=042a495e-998a4caf-b967-4030b7f5e7bf (Continued on next page) Cancer Cell 40, 1423–1439.e1–e11, November 14, 2022 e2

    Recombinase Polymerase Amplification:

    Article Title: Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc Receptor Binding Inhibitor polyclonal eBioscience/ThermoFisher Scientific Cat # 14-9161-73; RRID: AB_468582 Mouse monoclonal Anti-Human CD45 (Clone HI30) Fluidigm Cat # 3089003B; 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 Cleaved PARP (Clone F21-852) BD Biosciences Cat # 552596, RRID: AB_394437 Mouse monoclonal anti-human RORgt (Clone RORg2) BioLegend Cat # 646502, RRID: AB_2238503 Mouse monoclonal anti-human IgM (clone MHM-88) BioLegend Cat # 314502; RRID: AB_493003 Mouse monoclonal anti-human PICP (Clone PCIDG10) Millipore Cat # MAB1913, RRID: AB_94406 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 CD11b (Clone ICRF44) Fluidigm Cat # 3144001, RRID: AB_2714152 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 TCR Va7.2 (Clone 3C10) Biolegend Cat # 351702, RRID: AB_10900258 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 # 3151009B, RRID: AB_2810244 Mouse monoclonal anti-human TCRgd (Clone 11F2) Fluidigm Cat # 3152008B, RRID: AB_2687643 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 PD-L1 (clone 29E.2A3) Fluidigm Cat # 3156026, RRID: AB_2687855 Mouse monoclonal anti-human CD45RA (clone HI100) BioLegend Cat # 304102; RRID: AB_314406 Mouse monoclonal anti-human EMR1 (Clone BM8) Biolegend Cat # 123102, RRID: AB_893506 Mouse monoclonal anti-human FOXP3 (clone 259D/C7) Fluidigm Cat # 3159028A; RRID: AB_2811088 (Continued on next page) 16 Cell Reports 43, 114599, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-human T-bet (Clone 4B10) Fluidigm Cat # 3160010B, RRID: AB_2810251 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 CD15 (Clone W6D3) Biolegend Cat # 323002, RRID: AB_756008 Rabbit monoclonal anti-human phospho4E-BP1 (Thr37/Thr46) (clone 236B4) Cell Signaling Technology Cat # 2855; RRID: AB_560835 Mouse monoclonal anti-human CD27 (clone L128) Fluidigm Cat # 3167006B; RRID: AB_2811093 Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) Cell Signaling Technology Cat # 9167; RRID: AB_561284 Mouse monoclonal anti-human CD25 (clone 2A3) Fluidigm Cat # 3169003; RRID: AB_2661806 Mouse monoclonal anti-human CD33 (clone WM53) Biolegend Cat # 303402, RRID: AB_314346 Mouse monoclonal anti-human CD95 (clone DX2) Biolegend Cat # 305602, RRID: AB_314540 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 CD161 (clone DX12) BD Biosciences Cat # 556079, RRID: AB_396346 Mouse monoclonal anti-human CD56 (clone N901) Fluidigm Cat # 3176009B; RRID: AB_2811096 Critical commercial assays Vacutainer EDTA tubes BD Cat # 36643 PAXgene Blood RNA tubes Qiagen Cat # 762165 PAXgene Blood RNA Kit Qiagen Cat # 762164 Allprep DNA/RNA/miRNA Universal Kit Qiagen Cat # 80224 GlobinClear kit ThermoFisher Scientific Cat # AM1980 NEBNext Poly(A) mRNA Magnetic Isolation Module New England Biolabs Cat #E7490 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs Cat #E7760; V-PLEX Human Biomarker 54-Plex MesoScale Discovery Cat #K15248D Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 10X PBS, pH 7.2 Rockland Cat # MB-008 Cell Staining Buffer Fluidigm Cat # 201068 Cell-IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Cell-ID Intercalator-Ir Fluidigm Cat # 201192A Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B (Continued on next page) Cell Reports 43, 114599, August 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data HTP Sample/Participant metadata and co-occurring conditions Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488784 HTP whole blood RNA-seq data Galbraith et al.27 GEO: GSE190125, Synapse: https://doi. org/10.7303/syn31488780 HTP plasma proteomics data Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488781 HTP mass cytometry data Galbraith et al.27 Flow Repository: FR-FCM-Z5GE, Synapse: https://doi.org/10.7303/ syn31488783 HTP white blood cell RNA-seq data Powers et al.47 GEO: GSE251967 Mouse adult heart RNA-seq data Waugh et al.41 GEO: GSE218883 Mouse embryonic (E12.5) heart RNA-seq data Waugh et al.41 GEO: GSE218888 Mouse embyronic (E18.5) heart RNAseq data Waugh et al.41 GEO: GSE218889 Mouse adult whole brain RNA-seq data Waugh et al.41 GEO: GSE218885 Mouse adult brain hippocampus RNA-seq data This study GEO: GSE272567 Mouse adult brain cortex RNA-seq data This study GEO: GSE272568 Mouse adult kidney RNA-seq data This study GEO: GSE272569 Mouse adult liver RNA-seq data This study GEO: GSE272570 Mouse adult spleen RNA-seq data This study GEO: GSE272572 Mouse embryonic (E10.5) facial mesenchyme RNA-seq data Waugh et al.41 GEO: GSE218887 Mouse adult mesenteric lymph node RNA-seq data Waugh et al.41 GEO: GSE218890 Mouse adult lung RNA-seq data This study GEO: GSE229762 Software and algorithms R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 R Studio R Studio, Inc. v2023.09.1 + 494; RRID:SCR_000432 Bioconductor Bioconductor v3.17; RRID:SCR_006442 Tidyverse collection of packages for R CRAN RRID:SCR_019186 limma package for R Bioconductor v3.56.2; RRID:SCR_010943 FASTQC Babraham Institute v0.11.5; RRID:SCR_014583, https://www. bioinformatics.babraham.ac.uk/projects/ fastqc/ FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141, https://www. bioinformatics.babraham.ac.uk/projects/ fastq_screen/ bbduk/BBTools Bushnell et al.71 v37.99; RRID:SCR_016968, https://jgi. doe.gov/data-and-tools/bbtools/ fastq-mcf/ea-utils N/A v1.05; RRID:SCR_005553, https:// expressionanalysis.github.io/ea-utils/ HISAT2 Kim et al.72 v2.1.0; RRID:SCR_015530, https:// daehwankimlab.github.io/hisat2/ Human genome sequence primary assembly fasta Gencode GRCh38; RRID: SCR_014966, https:// www.gencodegenes.org/human/ release_33.html Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966, https://www. gencodegenes.org/human/release_33.html Samtools N/A v1.5; RRID: SCR_002105, http://www.htslib.org/ HTSeq-count N/A v0.6.1; RRID:SCR_005514, https://htseq. readthedocs.io/en/master/ (Continued on next page) 18 Cell Reports 43, 114599, August 27, 2024

    Isolation:

    Article Title: Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc Receptor Binding Inhibitor polyclonal eBioscience/ThermoFisher Scientific Cat # 14-9161-73; RRID: AB_468582 Mouse monoclonal Anti-Human CD45 (Clone HI30) Fluidigm Cat # 3089003B; 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 Cleaved PARP (Clone F21-852) BD Biosciences Cat # 552596, RRID: AB_394437 Mouse monoclonal anti-human RORgt (Clone RORg2) BioLegend Cat # 646502, RRID: AB_2238503 Mouse monoclonal anti-human IgM (clone MHM-88) BioLegend Cat # 314502; RRID: AB_493003 Mouse monoclonal anti-human PICP (Clone PCIDG10) Millipore Cat # MAB1913, RRID: AB_94406 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 CD11b (Clone ICRF44) Fluidigm Cat # 3144001, RRID: AB_2714152 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 TCR Va7.2 (Clone 3C10) Biolegend Cat # 351702, RRID: AB_10900258 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 # 3151009B, RRID: AB_2810244 Mouse monoclonal anti-human TCRgd (Clone 11F2) Fluidigm Cat # 3152008B, RRID: AB_2687643 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 PD-L1 (clone 29E.2A3) Fluidigm Cat # 3156026, RRID: AB_2687855 Mouse monoclonal anti-human CD45RA (clone HI100) BioLegend Cat # 304102; RRID: AB_314406 Mouse monoclonal anti-human EMR1 (Clone BM8) Biolegend Cat # 123102, RRID: AB_893506 Mouse monoclonal anti-human FOXP3 (clone 259D/C7) Fluidigm Cat # 3159028A; RRID: AB_2811088 (Continued on next page) 16 Cell Reports 43, 114599, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-human T-bet (Clone 4B10) Fluidigm Cat # 3160010B, RRID: AB_2810251 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 CD15 (Clone W6D3) Biolegend Cat # 323002, RRID: AB_756008 Rabbit monoclonal anti-human phospho4E-BP1 (Thr37/Thr46) (clone 236B4) Cell Signaling Technology Cat # 2855; RRID: AB_560835 Mouse monoclonal anti-human CD27 (clone L128) Fluidigm Cat # 3167006B; RRID: AB_2811093 Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) Cell Signaling Technology Cat # 9167; RRID: AB_561284 Mouse monoclonal anti-human CD25 (clone 2A3) Fluidigm Cat # 3169003; RRID: AB_2661806 Mouse monoclonal anti-human CD33 (clone WM53) Biolegend Cat # 303402, RRID: AB_314346 Mouse monoclonal anti-human CD95 (clone DX2) Biolegend Cat # 305602, RRID: AB_314540 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 CD161 (clone DX12) BD Biosciences Cat # 556079, RRID: AB_396346 Mouse monoclonal anti-human CD56 (clone N901) Fluidigm Cat # 3176009B; RRID: AB_2811096 Critical commercial assays Vacutainer EDTA tubes BD Cat # 36643 PAXgene Blood RNA tubes Qiagen Cat # 762165 PAXgene Blood RNA Kit Qiagen Cat # 762164 Allprep DNA/RNA/miRNA Universal Kit Qiagen Cat # 80224 GlobinClear kit ThermoFisher Scientific Cat # AM1980 NEBNext Poly(A) mRNA Magnetic Isolation Module New England Biolabs Cat #E7490 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs Cat #E7760; V-PLEX Human Biomarker 54-Plex MesoScale Discovery Cat #K15248D Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 10X PBS, pH 7.2 Rockland Cat # MB-008 Cell Staining Buffer Fluidigm Cat # 201068 Cell-IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Cell-ID Intercalator-Ir Fluidigm Cat # 201192A Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B (Continued on next page) Cell Reports 43, 114599, August 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data HTP Sample/Participant metadata and co-occurring conditions Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488784 HTP whole blood RNA-seq data Galbraith et al.27 GEO: GSE190125, Synapse: https://doi. org/10.7303/syn31488780 HTP plasma proteomics data Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488781 HTP mass cytometry data Galbraith et al.27 Flow Repository: FR-FCM-Z5GE, Synapse: https://doi.org/10.7303/ syn31488783 HTP white blood cell RNA-seq data Powers et al.47 GEO: GSE251967 Mouse adult heart RNA-seq data Waugh et al.41 GEO: GSE218883 Mouse embryonic (E12.5) heart RNA-seq data Waugh et al.41 GEO: GSE218888 Mouse embyronic (E18.5) heart RNAseq data Waugh et al.41 GEO: GSE218889 Mouse adult whole brain RNA-seq data Waugh et al.41 GEO: GSE218885 Mouse adult brain hippocampus RNA-seq data This study GEO: GSE272567 Mouse adult brain cortex RNA-seq data This study GEO: GSE272568 Mouse adult kidney RNA-seq data This study GEO: GSE272569 Mouse adult liver RNA-seq data This study GEO: GSE272570 Mouse adult spleen RNA-seq data This study GEO: GSE272572 Mouse embryonic (E10.5) facial mesenchyme RNA-seq data Waugh et al.41 GEO: GSE218887 Mouse adult mesenteric lymph node RNA-seq data Waugh et al.41 GEO: GSE218890 Mouse adult lung RNA-seq data This study GEO: GSE229762 Software and algorithms R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 R Studio R Studio, Inc. v2023.09.1 + 494; RRID:SCR_000432 Bioconductor Bioconductor v3.17; RRID:SCR_006442 Tidyverse collection of packages for R CRAN RRID:SCR_019186 limma package for R Bioconductor v3.56.2; RRID:SCR_010943 FASTQC Babraham Institute v0.11.5; RRID:SCR_014583, https://www. bioinformatics.babraham.ac.uk/projects/ fastqc/ FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141, https://www. bioinformatics.babraham.ac.uk/projects/ fastq_screen/ bbduk/BBTools Bushnell et al.71 v37.99; RRID:SCR_016968, https://jgi. doe.gov/data-and-tools/bbtools/ fastq-mcf/ea-utils N/A v1.05; RRID:SCR_005553, https:// expressionanalysis.github.io/ea-utils/ HISAT2 Kim et al.72 v2.1.0; RRID:SCR_015530, https:// daehwankimlab.github.io/hisat2/ Human genome sequence primary assembly fasta Gencode GRCh38; RRID: SCR_014966, https:// www.gencodegenes.org/human/ release_33.html Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966, https://www. gencodegenes.org/human/release_33.html Samtools N/A v1.5; RRID: SCR_002105, http://www.htslib.org/ HTSeq-count N/A v0.6.1; RRID:SCR_005514, https://htseq. readthedocs.io/en/master/ (Continued on next page) 18 Cell Reports 43, 114599, August 27, 2024

    Biomarker Discovery:

    Article Title: Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc Receptor Binding Inhibitor polyclonal eBioscience/ThermoFisher Scientific Cat # 14-9161-73; RRID: AB_468582 Mouse monoclonal Anti-Human CD45 (Clone HI30) Fluidigm Cat # 3089003B; 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 Cleaved PARP (Clone F21-852) BD Biosciences Cat # 552596, RRID: AB_394437 Mouse monoclonal anti-human RORgt (Clone RORg2) BioLegend Cat # 646502, RRID: AB_2238503 Mouse monoclonal anti-human IgM (clone MHM-88) BioLegend Cat # 314502; RRID: AB_493003 Mouse monoclonal anti-human PICP (Clone PCIDG10) Millipore Cat # MAB1913, RRID: AB_94406 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 CD11b (Clone ICRF44) Fluidigm Cat # 3144001, RRID: AB_2714152 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 TCR Va7.2 (Clone 3C10) Biolegend Cat # 351702, RRID: AB_10900258 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 # 3151009B, RRID: AB_2810244 Mouse monoclonal anti-human TCRgd (Clone 11F2) Fluidigm Cat # 3152008B, RRID: AB_2687643 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 PD-L1 (clone 29E.2A3) Fluidigm Cat # 3156026, RRID: AB_2687855 Mouse monoclonal anti-human CD45RA (clone HI100) BioLegend Cat # 304102; RRID: AB_314406 Mouse monoclonal anti-human EMR1 (Clone BM8) Biolegend Cat # 123102, RRID: AB_893506 Mouse monoclonal anti-human FOXP3 (clone 259D/C7) Fluidigm Cat # 3159028A; RRID: AB_2811088 (Continued on next page) 16 Cell Reports 43, 114599, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-human T-bet (Clone 4B10) Fluidigm Cat # 3160010B, RRID: AB_2810251 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 CD15 (Clone W6D3) Biolegend Cat # 323002, RRID: AB_756008 Rabbit monoclonal anti-human phospho4E-BP1 (Thr37/Thr46) (clone 236B4) Cell Signaling Technology Cat # 2855; RRID: AB_560835 Mouse monoclonal anti-human CD27 (clone L128) Fluidigm Cat # 3167006B; RRID: AB_2811093 Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) Cell Signaling Technology Cat # 9167; RRID: AB_561284 Mouse monoclonal anti-human CD25 (clone 2A3) Fluidigm Cat # 3169003; RRID: AB_2661806 Mouse monoclonal anti-human CD33 (clone WM53) Biolegend Cat # 303402, RRID: AB_314346 Mouse monoclonal anti-human CD95 (clone DX2) Biolegend Cat # 305602, RRID: AB_314540 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 CD161 (clone DX12) BD Biosciences Cat # 556079, RRID: AB_396346 Mouse monoclonal anti-human CD56 (clone N901) Fluidigm Cat # 3176009B; RRID: AB_2811096 Critical commercial assays Vacutainer EDTA tubes BD Cat # 36643 PAXgene Blood RNA tubes Qiagen Cat # 762165 PAXgene Blood RNA Kit Qiagen Cat # 762164 Allprep DNA/RNA/miRNA Universal Kit Qiagen Cat # 80224 GlobinClear kit ThermoFisher Scientific Cat # AM1980 NEBNext Poly(A) mRNA Magnetic Isolation Module New England Biolabs Cat #E7490 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs Cat #E7760; V-PLEX Human Biomarker 54-Plex MesoScale Discovery Cat #K15248D Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 10X PBS, pH 7.2 Rockland Cat # MB-008 Cell Staining Buffer Fluidigm Cat # 201068 Cell-IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Cell-ID Intercalator-Ir Fluidigm Cat # 201192A Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B (Continued on next page) Cell Reports 43, 114599, August 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data HTP Sample/Participant metadata and co-occurring conditions Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488784 HTP whole blood RNA-seq data Galbraith et al.27 GEO: GSE190125, Synapse: https://doi. org/10.7303/syn31488780 HTP plasma proteomics data Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488781 HTP mass cytometry data Galbraith et al.27 Flow Repository: FR-FCM-Z5GE, Synapse: https://doi.org/10.7303/ syn31488783 HTP white blood cell RNA-seq data Powers et al.47 GEO: GSE251967 Mouse adult heart RNA-seq data Waugh et al.41 GEO: GSE218883 Mouse embryonic (E12.5) heart RNA-seq data Waugh et al.41 GEO: GSE218888 Mouse embyronic (E18.5) heart RNAseq data Waugh et al.41 GEO: GSE218889 Mouse adult whole brain RNA-seq data Waugh et al.41 GEO: GSE218885 Mouse adult brain hippocampus RNA-seq data This study GEO: GSE272567 Mouse adult brain cortex RNA-seq data This study GEO: GSE272568 Mouse adult kidney RNA-seq data This study GEO: GSE272569 Mouse adult liver RNA-seq data This study GEO: GSE272570 Mouse adult spleen RNA-seq data This study GEO: GSE272572 Mouse embryonic (E10.5) facial mesenchyme RNA-seq data Waugh et al.41 GEO: GSE218887 Mouse adult mesenteric lymph node RNA-seq data Waugh et al.41 GEO: GSE218890 Mouse adult lung RNA-seq data This study GEO: GSE229762 Software and algorithms R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 R Studio R Studio, Inc. v2023.09.1 + 494; RRID:SCR_000432 Bioconductor Bioconductor v3.17; RRID:SCR_006442 Tidyverse collection of packages for R CRAN RRID:SCR_019186 limma package for R Bioconductor v3.56.2; RRID:SCR_010943 FASTQC Babraham Institute v0.11.5; RRID:SCR_014583, https://www. bioinformatics.babraham.ac.uk/projects/ fastqc/ FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141, https://www. bioinformatics.babraham.ac.uk/projects/ fastq_screen/ bbduk/BBTools Bushnell et al.71 v37.99; RRID:SCR_016968, https://jgi. doe.gov/data-and-tools/bbtools/ fastq-mcf/ea-utils N/A v1.05; RRID:SCR_005553, https:// expressionanalysis.github.io/ea-utils/ HISAT2 Kim et al.72 v2.1.0; RRID:SCR_015530, https:// daehwankimlab.github.io/hisat2/ Human genome sequence primary assembly fasta Gencode GRCh38; RRID: SCR_014966, https:// www.gencodegenes.org/human/ release_33.html Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966, https://www. gencodegenes.org/human/release_33.html Samtools N/A v1.5; RRID: SCR_002105, http://www.htslib.org/ HTSeq-count N/A v0.6.1; RRID:SCR_005514, https://htseq. readthedocs.io/en/master/ (Continued on next page) 18 Cell Reports 43, 114599, August 27, 2024

    Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome
    Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit V- PLEX Human Biomarker 54- Plex MesoScale Discovery Cat # K15248D Commercial assay or kit Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 Commercial assay or kit Cell Staining Buffer Fluidigm Cat # 201068 Commercial assay or kit Cell- IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Commercial assay or kit Cell- ID Intercalator- Ir Fluidigm Cat # 201192 A Commercial assay or kit Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B Software, algorithm R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 Software, algorithm R Studio R Studio, Inc v2023.09.1+494; RRID:SCR_000432 Software, algorithm Bioconductor Bioconductor v3.17; RRID:SCR_006442 Software, algorithm Tidyverse collection of packages for R CRAN RRID:SCR_019186 Software, algorithm limma package for R Bioconductor v3.56.2; RRID:SCR_010943 Software, algorithm FASTQC Babraham Institute v0.11.5; RRID:SCR_014583 Software, algorithm FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141 Software, algorithm bbduk/BBTools Bushnell et al., 2017 v37.99; RRID:SCR_016968 Software, algorithm fastq- mcf/ea- utils N/A v1.05; RRID:SCR_005553 Software, algorithm HISAT2 Kim et al., 2019 v2.1.0; RRID:SCR_015530 Software, algorithm Human genome sequence primary assembly fasta Gencode GRCh38; RRID:SCR_014966 Software, algorithm Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966 Software, algorithm Samtools N/A v1.5; RRID:SCR_002105 Software, algorithm HTSeq- count N/A v0.6.1; RRID:SCR_005514 Software, algorithm DESeq2 package for R Bioconductor v1.28.1; RRID:SCR_015687 Software, algorithm fgsea package for R Bioconductor v1.26.0; RRID:SCR_020938 Software, algorithm Hmisc package for R CRAN V5.1.1; RRID:SCR_022497 Software, algorithm ggplot2 package for R CRAN v3.4.4; RRID:SCR_014601 Software, algorithm rstatix package for R CRAN v0.7.2; RRID:SCR_021240 Software, algorithm ComplexHeatmap package for R CRAN v2.4.2; RRID:SCR_017270 Software, algorithm tidyheatmap package for R CRAN V1.8.1 Software, algorithm ggforce package for R CRAN v0.4.1 Software, algorithm CellEngine CellCarta, Montreal, Canada RRID:SCR_022484 Software, algorithm flowCore package for R Hahne et al., 2009; Bioconductor v2.0.1; RRID:SCR_002205 Software, algorithm CATALYST package for R Chevrier et al., 2018; Bioconductor v1.12.2; RRID:SCR_017127 Appendix 1 Continued Appendix 1 Continued on next page Rachubinski et al. eLife 2024;13:RP99323. ..

    Staining:

    Article Title: Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc Receptor Binding Inhibitor polyclonal eBioscience/ThermoFisher Scientific Cat # 14-9161-73; RRID: AB_468582 Mouse monoclonal Anti-Human CD45 (Clone HI30) Fluidigm Cat # 3089003B; 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 Cleaved PARP (Clone F21-852) BD Biosciences Cat # 552596, RRID: AB_394437 Mouse monoclonal anti-human RORgt (Clone RORg2) BioLegend Cat # 646502, RRID: AB_2238503 Mouse monoclonal anti-human IgM (clone MHM-88) BioLegend Cat # 314502; RRID: AB_493003 Mouse monoclonal anti-human PICP (Clone PCIDG10) Millipore Cat # MAB1913, RRID: AB_94406 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 CD11b (Clone ICRF44) Fluidigm Cat # 3144001, RRID: AB_2714152 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 TCR Va7.2 (Clone 3C10) Biolegend Cat # 351702, RRID: AB_10900258 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 # 3151009B, RRID: AB_2810244 Mouse monoclonal anti-human TCRgd (Clone 11F2) Fluidigm Cat # 3152008B, RRID: AB_2687643 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 PD-L1 (clone 29E.2A3) Fluidigm Cat # 3156026, RRID: AB_2687855 Mouse monoclonal anti-human CD45RA (clone HI100) BioLegend Cat # 304102; RRID: AB_314406 Mouse monoclonal anti-human EMR1 (Clone BM8) Biolegend Cat # 123102, RRID: AB_893506 Mouse monoclonal anti-human FOXP3 (clone 259D/C7) Fluidigm Cat # 3159028A; RRID: AB_2811088 (Continued on next page) 16 Cell Reports 43, 114599, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-human T-bet (Clone 4B10) Fluidigm Cat # 3160010B, RRID: AB_2810251 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 CD15 (Clone W6D3) Biolegend Cat # 323002, RRID: AB_756008 Rabbit monoclonal anti-human phospho4E-BP1 (Thr37/Thr46) (clone 236B4) Cell Signaling Technology Cat # 2855; RRID: AB_560835 Mouse monoclonal anti-human CD27 (clone L128) Fluidigm Cat # 3167006B; RRID: AB_2811093 Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) Cell Signaling Technology Cat # 9167; RRID: AB_561284 Mouse monoclonal anti-human CD25 (clone 2A3) Fluidigm Cat # 3169003; RRID: AB_2661806 Mouse monoclonal anti-human CD33 (clone WM53) Biolegend Cat # 303402, RRID: AB_314346 Mouse monoclonal anti-human CD95 (clone DX2) Biolegend Cat # 305602, RRID: AB_314540 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 CD161 (clone DX12) BD Biosciences Cat # 556079, RRID: AB_396346 Mouse monoclonal anti-human CD56 (clone N901) Fluidigm Cat # 3176009B; RRID: AB_2811096 Critical commercial assays Vacutainer EDTA tubes BD Cat # 36643 PAXgene Blood RNA tubes Qiagen Cat # 762165 PAXgene Blood RNA Kit Qiagen Cat # 762164 Allprep DNA/RNA/miRNA Universal Kit Qiagen Cat # 80224 GlobinClear kit ThermoFisher Scientific Cat # AM1980 NEBNext Poly(A) mRNA Magnetic Isolation Module New England Biolabs Cat #E7490 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs Cat #E7760; V-PLEX Human Biomarker 54-Plex MesoScale Discovery Cat #K15248D Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 10X PBS, pH 7.2 Rockland Cat # MB-008 Cell Staining Buffer Fluidigm Cat # 201068 Cell-IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Cell-ID Intercalator-Ir Fluidigm Cat # 201192A Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B (Continued on next page) Cell Reports 43, 114599, August 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data HTP Sample/Participant metadata and co-occurring conditions Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488784 HTP whole blood RNA-seq data Galbraith et al.27 GEO: GSE190125, Synapse: https://doi. org/10.7303/syn31488780 HTP plasma proteomics data Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488781 HTP mass cytometry data Galbraith et al.27 Flow Repository: FR-FCM-Z5GE, Synapse: https://doi.org/10.7303/ syn31488783 HTP white blood cell RNA-seq data Powers et al.47 GEO: GSE251967 Mouse adult heart RNA-seq data Waugh et al.41 GEO: GSE218883 Mouse embryonic (E12.5) heart RNA-seq data Waugh et al.41 GEO: GSE218888 Mouse embyronic (E18.5) heart RNAseq data Waugh et al.41 GEO: GSE218889 Mouse adult whole brain RNA-seq data Waugh et al.41 GEO: GSE218885 Mouse adult brain hippocampus RNA-seq data This study GEO: GSE272567 Mouse adult brain cortex RNA-seq data This study GEO: GSE272568 Mouse adult kidney RNA-seq data This study GEO: GSE272569 Mouse adult liver RNA-seq data This study GEO: GSE272570 Mouse adult spleen RNA-seq data This study GEO: GSE272572 Mouse embryonic (E10.5) facial mesenchyme RNA-seq data Waugh et al.41 GEO: GSE218887 Mouse adult mesenteric lymph node RNA-seq data Waugh et al.41 GEO: GSE218890 Mouse adult lung RNA-seq data This study GEO: GSE229762 Software and algorithms R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 R Studio R Studio, Inc. v2023.09.1 + 494; RRID:SCR_000432 Bioconductor Bioconductor v3.17; RRID:SCR_006442 Tidyverse collection of packages for R CRAN RRID:SCR_019186 limma package for R Bioconductor v3.56.2; RRID:SCR_010943 FASTQC Babraham Institute v0.11.5; RRID:SCR_014583, https://www. bioinformatics.babraham.ac.uk/projects/ fastqc/ FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141, https://www. bioinformatics.babraham.ac.uk/projects/ fastq_screen/ bbduk/BBTools Bushnell et al.71 v37.99; RRID:SCR_016968, https://jgi. doe.gov/data-and-tools/bbtools/ fastq-mcf/ea-utils N/A v1.05; RRID:SCR_005553, https:// expressionanalysis.github.io/ea-utils/ HISAT2 Kim et al.72 v2.1.0; RRID:SCR_015530, https:// daehwankimlab.github.io/hisat2/ Human genome sequence primary assembly fasta Gencode GRCh38; RRID: SCR_014966, https:// www.gencodegenes.org/human/ release_33.html Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966, https://www. gencodegenes.org/human/release_33.html Samtools N/A v1.5; RRID: SCR_002105, http://www.htslib.org/ HTSeq-count N/A v0.6.1; RRID:SCR_005514, https://htseq. readthedocs.io/en/master/ (Continued on next page) 18 Cell Reports 43, 114599, August 27, 2024

    Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome
    Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit V- PLEX Human Biomarker 54- Plex MesoScale Discovery Cat # K15248D Commercial assay or kit Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 Commercial assay or kit Cell Staining Buffer Fluidigm Cat # 201068 Commercial assay or kit Cell- IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Commercial assay or kit Cell- ID Intercalator- Ir Fluidigm Cat # 201192 A Commercial assay or kit Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B Software, algorithm R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 Software, algorithm R Studio R Studio, Inc v2023.09.1+494; RRID:SCR_000432 Software, algorithm Bioconductor Bioconductor v3.17; RRID:SCR_006442 Software, algorithm Tidyverse collection of packages for R CRAN RRID:SCR_019186 Software, algorithm limma package for R Bioconductor v3.56.2; RRID:SCR_010943 Software, algorithm FASTQC Babraham Institute v0.11.5; RRID:SCR_014583 Software, algorithm FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141 Software, algorithm bbduk/BBTools Bushnell et al., 2017 v37.99; RRID:SCR_016968 Software, algorithm fastq- mcf/ea- utils N/A v1.05; RRID:SCR_005553 Software, algorithm HISAT2 Kim et al., 2019 v2.1.0; RRID:SCR_015530 Software, algorithm Human genome sequence primary assembly fasta Gencode GRCh38; RRID:SCR_014966 Software, algorithm Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966 Software, algorithm Samtools N/A v1.5; RRID:SCR_002105 Software, algorithm HTSeq- count N/A v0.6.1; RRID:SCR_005514 Software, algorithm DESeq2 package for R Bioconductor v1.28.1; RRID:SCR_015687 Software, algorithm fgsea package for R Bioconductor v1.26.0; RRID:SCR_020938 Software, algorithm Hmisc package for R CRAN V5.1.1; RRID:SCR_022497 Software, algorithm ggplot2 package for R CRAN v3.4.4; RRID:SCR_014601 Software, algorithm rstatix package for R CRAN v0.7.2; RRID:SCR_021240 Software, algorithm ComplexHeatmap package for R CRAN v2.4.2; RRID:SCR_017270 Software, algorithm tidyheatmap package for R CRAN V1.8.1 Software, algorithm ggforce package for R CRAN v0.4.1 Software, algorithm CellEngine CellCarta, Montreal, Canada RRID:SCR_022484 Software, algorithm flowCore package for R Hahne et al., 2009; Bioconductor v2.0.1; RRID:SCR_002205 Software, algorithm CATALYST package for R Chevrier et al., 2018; Bioconductor v1.12.2; RRID:SCR_017127 Appendix 1 Continued Appendix 1 Continued on next page Rachubinski et al. eLife 2024;13:RP99323. ..

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Antibody Labeling:

    Article Title: Multimodal analysis of dysregulated heme metabolism, hypoxic signaling, and stress erythropoiesis in Down syndrome.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc Receptor Binding Inhibitor polyclonal eBioscience/ThermoFisher Scientific Cat # 14-9161-73; RRID: AB_468582 Mouse monoclonal Anti-Human CD45 (Clone HI30) Fluidigm Cat # 3089003B; 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 Cleaved PARP (Clone F21-852) BD Biosciences Cat # 552596, RRID: AB_394437 Mouse monoclonal anti-human RORgt (Clone RORg2) BioLegend Cat # 646502, RRID: AB_2238503 Mouse monoclonal anti-human IgM (clone MHM-88) BioLegend Cat # 314502; RRID: AB_493003 Mouse monoclonal anti-human PICP (Clone PCIDG10) Millipore Cat # MAB1913, RRID: AB_94406 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 CD11b (Clone ICRF44) Fluidigm Cat # 3144001, RRID: AB_2714152 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 TCR Va7.2 (Clone 3C10) Biolegend Cat # 351702, RRID: AB_10900258 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 # 3151009B, RRID: AB_2810244 Mouse monoclonal anti-human TCRgd (Clone 11F2) Fluidigm Cat # 3152008B, RRID: AB_2687643 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 PD-L1 (clone 29E.2A3) Fluidigm Cat # 3156026, RRID: AB_2687855 Mouse monoclonal anti-human CD45RA (clone HI100) BioLegend Cat # 304102; RRID: AB_314406 Mouse monoclonal anti-human EMR1 (Clone BM8) Biolegend Cat # 123102, RRID: AB_893506 Mouse monoclonal anti-human FOXP3 (clone 259D/C7) Fluidigm Cat # 3159028A; RRID: AB_2811088 (Continued on next page) 16 Cell Reports 43, 114599, August 27, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mouse monoclonal anti-human T-bet (Clone 4B10) Fluidigm Cat # 3160010B, RRID: AB_2810251 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 CD15 (Clone W6D3) Biolegend Cat # 323002, RRID: AB_756008 Rabbit monoclonal anti-human phospho4E-BP1 (Thr37/Thr46) (clone 236B4) Cell Signaling Technology Cat # 2855; RRID: AB_560835 Mouse monoclonal anti-human CD27 (clone L128) Fluidigm Cat # 3167006B; RRID: AB_2811093 Rabbit monoclonal anti-human phospho-STAT1 (Tyr701) (clone 58D6) Cell Signaling Technology Cat # 9167; RRID: AB_561284 Mouse monoclonal anti-human CD25 (clone 2A3) Fluidigm Cat # 3169003; RRID: AB_2661806 Mouse monoclonal anti-human CD33 (clone WM53) Biolegend Cat # 303402, RRID: AB_314346 Mouse monoclonal anti-human CD95 (clone DX2) Biolegend Cat # 305602, RRID: AB_314540 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 CD161 (clone DX12) BD Biosciences Cat # 556079, RRID: AB_396346 Mouse monoclonal anti-human CD56 (clone N901) Fluidigm Cat # 3176009B; RRID: AB_2811096 Critical commercial assays Vacutainer EDTA tubes BD Cat # 36643 PAXgene Blood RNA tubes Qiagen Cat # 762165 PAXgene Blood RNA Kit Qiagen Cat # 762164 Allprep DNA/RNA/miRNA Universal Kit Qiagen Cat # 80224 GlobinClear kit ThermoFisher Scientific Cat # AM1980 NEBNext Poly(A) mRNA Magnetic Isolation Module New England Biolabs Cat #E7490 NEBNext Ultra II Directional RNA Library Prep Kit for Illumina New England Biolabs Cat #E7760; V-PLEX Human Biomarker 54-Plex MesoScale Discovery Cat #K15248D Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 10X PBS, pH 7.2 Rockland Cat # MB-008 Cell Staining Buffer Fluidigm Cat # 201068 Cell-IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Cell-ID Intercalator-Ir Fluidigm Cat # 201192A Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B (Continued on next page) Cell Reports 43, 114599, August 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data HTP Sample/Participant metadata and co-occurring conditions Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488784 HTP whole blood RNA-seq data Galbraith et al.27 GEO: GSE190125, Synapse: https://doi. org/10.7303/syn31488780 HTP plasma proteomics data Galbraith et al.27 Synapse: https://doi.org/10.7303/ syn31488781 HTP mass cytometry data Galbraith et al.27 Flow Repository: FR-FCM-Z5GE, Synapse: https://doi.org/10.7303/ syn31488783 HTP white blood cell RNA-seq data Powers et al.47 GEO: GSE251967 Mouse adult heart RNA-seq data Waugh et al.41 GEO: GSE218883 Mouse embryonic (E12.5) heart RNA-seq data Waugh et al.41 GEO: GSE218888 Mouse embyronic (E18.5) heart RNAseq data Waugh et al.41 GEO: GSE218889 Mouse adult whole brain RNA-seq data Waugh et al.41 GEO: GSE218885 Mouse adult brain hippocampus RNA-seq data This study GEO: GSE272567 Mouse adult brain cortex RNA-seq data This study GEO: GSE272568 Mouse adult kidney RNA-seq data This study GEO: GSE272569 Mouse adult liver RNA-seq data This study GEO: GSE272570 Mouse adult spleen RNA-seq data This study GEO: GSE272572 Mouse embryonic (E10.5) facial mesenchyme RNA-seq data Waugh et al.41 GEO: GSE218887 Mouse adult mesenteric lymph node RNA-seq data Waugh et al.41 GEO: GSE218890 Mouse adult lung RNA-seq data This study GEO: GSE229762 Software and algorithms R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 R Studio R Studio, Inc. v2023.09.1 + 494; RRID:SCR_000432 Bioconductor Bioconductor v3.17; RRID:SCR_006442 Tidyverse collection of packages for R CRAN RRID:SCR_019186 limma package for R Bioconductor v3.56.2; RRID:SCR_010943 FASTQC Babraham Institute v0.11.5; RRID:SCR_014583, https://www. bioinformatics.babraham.ac.uk/projects/ fastqc/ FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141, https://www. bioinformatics.babraham.ac.uk/projects/ fastq_screen/ bbduk/BBTools Bushnell et al.71 v37.99; RRID:SCR_016968, https://jgi. doe.gov/data-and-tools/bbtools/ fastq-mcf/ea-utils N/A v1.05; RRID:SCR_005553, https:// expressionanalysis.github.io/ea-utils/ HISAT2 Kim et al.72 v2.1.0; RRID:SCR_015530, https:// daehwankimlab.github.io/hisat2/ Human genome sequence primary assembly fasta Gencode GRCh38; RRID: SCR_014966, https:// www.gencodegenes.org/human/ release_33.html Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966, https://www. gencodegenes.org/human/release_33.html Samtools N/A v1.5; RRID: SCR_002105, http://www.htslib.org/ HTSeq-count N/A v0.6.1; RRID:SCR_005514, https://htseq. readthedocs.io/en/master/ (Continued on next page) 18 Cell Reports 43, 114599, August 27, 2024

    Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome
    Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit V- PLEX Human Biomarker 54- Plex MesoScale Discovery Cat # K15248D Commercial assay or kit Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 Commercial assay or kit Cell Staining Buffer Fluidigm Cat # 201068 Commercial assay or kit Cell- IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Commercial assay or kit Cell- ID Intercalator- Ir Fluidigm Cat # 201192 A Commercial assay or kit Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B Software, algorithm R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 Software, algorithm R Studio R Studio, Inc v2023.09.1+494; RRID:SCR_000432 Software, algorithm Bioconductor Bioconductor v3.17; RRID:SCR_006442 Software, algorithm Tidyverse collection of packages for R CRAN RRID:SCR_019186 Software, algorithm limma package for R Bioconductor v3.56.2; RRID:SCR_010943 Software, algorithm FASTQC Babraham Institute v0.11.5; RRID:SCR_014583 Software, algorithm FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141 Software, algorithm bbduk/BBTools Bushnell et al., 2017 v37.99; RRID:SCR_016968 Software, algorithm fastq- mcf/ea- utils N/A v1.05; RRID:SCR_005553 Software, algorithm HISAT2 Kim et al., 2019 v2.1.0; RRID:SCR_015530 Software, algorithm Human genome sequence primary assembly fasta Gencode GRCh38; RRID:SCR_014966 Software, algorithm Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966 Software, algorithm Samtools N/A v1.5; RRID:SCR_002105 Software, algorithm HTSeq- count N/A v0.6.1; RRID:SCR_005514 Software, algorithm DESeq2 package for R Bioconductor v1.28.1; RRID:SCR_015687 Software, algorithm fgsea package for R Bioconductor v1.26.0; RRID:SCR_020938 Software, algorithm Hmisc package for R CRAN V5.1.1; RRID:SCR_022497 Software, algorithm ggplot2 package for R CRAN v3.4.4; RRID:SCR_014601 Software, algorithm rstatix package for R CRAN v0.7.2; RRID:SCR_021240 Software, algorithm ComplexHeatmap package for R CRAN v2.4.2; RRID:SCR_017270 Software, algorithm tidyheatmap package for R CRAN V1.8.1 Software, algorithm ggforce package for R CRAN v0.4.1 Software, algorithm CellEngine CellCarta, Montreal, Canada RRID:SCR_022484 Software, algorithm flowCore package for R Hahne et al., 2009; Bioconductor v2.0.1; RRID:SCR_002205 Software, algorithm CATALYST package for R Chevrier et al., 2018; Bioconductor v1.12.2; RRID:SCR_017127 Appendix 1 Continued Appendix 1 Continued on next page Rachubinski et al. eLife 2024;13:RP99323. ..

    Software:

    Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome
    Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit V- PLEX Human Biomarker 54- Plex MesoScale Discovery Cat # K15248D Commercial assay or kit Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 Commercial assay or kit Cell Staining Buffer Fluidigm Cat # 201068 Commercial assay or kit Cell- IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Commercial assay or kit Cell- ID Intercalator- Ir Fluidigm Cat # 201192 A Commercial assay or kit Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B Software, algorithm R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 Software, algorithm R Studio R Studio, Inc v2023.09.1+494; RRID:SCR_000432 Software, algorithm Bioconductor Bioconductor v3.17; RRID:SCR_006442 Software, algorithm Tidyverse collection of packages for R CRAN RRID:SCR_019186 Software, algorithm limma package for R Bioconductor v3.56.2; RRID:SCR_010943 Software, algorithm FASTQC Babraham Institute v0.11.5; RRID:SCR_014583 Software, algorithm FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141 Software, algorithm bbduk/BBTools Bushnell et al., 2017 v37.99; RRID:SCR_016968 Software, algorithm fastq- mcf/ea- utils N/A v1.05; RRID:SCR_005553 Software, algorithm HISAT2 Kim et al., 2019 v2.1.0; RRID:SCR_015530 Software, algorithm Human genome sequence primary assembly fasta Gencode GRCh38; RRID:SCR_014966 Software, algorithm Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966 Software, algorithm Samtools N/A v1.5; RRID:SCR_002105 Software, algorithm HTSeq- count N/A v0.6.1; RRID:SCR_005514 Software, algorithm DESeq2 package for R Bioconductor v1.28.1; RRID:SCR_015687 Software, algorithm fgsea package for R Bioconductor v1.26.0; RRID:SCR_020938 Software, algorithm Hmisc package for R CRAN V5.1.1; RRID:SCR_022497 Software, algorithm ggplot2 package for R CRAN v3.4.4; RRID:SCR_014601 Software, algorithm rstatix package for R CRAN v0.7.2; RRID:SCR_021240 Software, algorithm ComplexHeatmap package for R CRAN v2.4.2; RRID:SCR_017270 Software, algorithm tidyheatmap package for R CRAN V1.8.1 Software, algorithm ggforce package for R CRAN v0.4.1 Software, algorithm CellEngine CellCarta, Montreal, Canada RRID:SCR_022484 Software, algorithm flowCore package for R Hahne et al., 2009; Bioconductor v2.0.1; RRID:SCR_002205 Software, algorithm CATALYST package for R Chevrier et al., 2018; Bioconductor v1.12.2; RRID:SCR_017127 Appendix 1 Continued Appendix 1 Continued on next page Rachubinski et al. eLife 2024;13:RP99323. ..

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Sequencing:

    Article Title: JAK inhibition decreases the autoimmune burden in Down syndrome
    Article Snippet: .. (species) or resource Designation Source or reference Identifiers Additional information Commercial assay or kit V- PLEX Human Biomarker 54- Plex MesoScale Discovery Cat # K15248D Commercial assay or kit Transcription Factor Phospho Buffer Set BD Pharmingen Cat # 563239 Commercial assay or kit Cell Staining Buffer Fluidigm Cat # 201068 Commercial assay or kit Cell- IDTM 20- Plex Pd Barcoding Kit Fluidigm Cat # PRD023 Commercial assay or kit Cell- ID Intercalator- Ir Fluidigm Cat # 201192 A Commercial assay or kit Maxpar Antibody Labeling Kit Fluidigm Cat # 201160B Software, algorithm R R Foundation for Statistical Computing v4.3.1; RRID:SCR_001905 Software, algorithm R Studio R Studio, Inc v2023.09.1+494; RRID:SCR_000432 Software, algorithm Bioconductor Bioconductor v3.17; RRID:SCR_006442 Software, algorithm Tidyverse collection of packages for R CRAN RRID:SCR_019186 Software, algorithm limma package for R Bioconductor v3.56.2; RRID:SCR_010943 Software, algorithm FASTQC Babraham Institute v0.11.5; RRID:SCR_014583 Software, algorithm FastQ Screen Babraham Institute v0.11.0; RRID:SCR_000141 Software, algorithm bbduk/BBTools Bushnell et al., 2017 v37.99; RRID:SCR_016968 Software, algorithm fastq- mcf/ea- utils N/A v1.05; RRID:SCR_005553 Software, algorithm HISAT2 Kim et al., 2019 v2.1.0; RRID:SCR_015530 Software, algorithm Human genome sequence primary assembly fasta Gencode GRCh38; RRID:SCR_014966 Software, algorithm Human genome basic annotation GTF file Gencode v33; RRID:SCR_014966 Software, algorithm Samtools N/A v1.5; RRID:SCR_002105 Software, algorithm HTSeq- count N/A v0.6.1; RRID:SCR_005514 Software, algorithm DESeq2 package for R Bioconductor v1.28.1; RRID:SCR_015687 Software, algorithm fgsea package for R Bioconductor v1.26.0; RRID:SCR_020938 Software, algorithm Hmisc package for R CRAN V5.1.1; RRID:SCR_022497 Software, algorithm ggplot2 package for R CRAN v3.4.4; RRID:SCR_014601 Software, algorithm rstatix package for R CRAN v0.7.2; RRID:SCR_021240 Software, algorithm ComplexHeatmap package for R CRAN v2.4.2; RRID:SCR_017270 Software, algorithm tidyheatmap package for R CRAN V1.8.1 Software, algorithm ggforce package for R CRAN v0.4.1 Software, algorithm CellEngine CellCarta, Montreal, Canada RRID:SCR_022484 Software, algorithm flowCore package for R Hahne et al., 2009; Bioconductor v2.0.1; RRID:SCR_002205 Software, algorithm CATALYST package for R Chevrier et al., 2018; Bioconductor v1.12.2; RRID:SCR_017127 Appendix 1 Continued Appendix 1 Continued on next page Rachubinski et al. eLife 2024;13:RP99323. ..

    High Performance Liquid Chromatography:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Recombinant:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Transfection:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Gene Expression:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Quantitative RT-PCR:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Expressing:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..

    Plasmid Preparation:

    Article Title: Lipid-associated macrophages reshape BAT cell identity in obesity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies 4 Hydroxynonenal antibody, Abcam Abcam Cat# ab46545, RRID: AB_722490 Anti-CD36 antibody Abcam Cat# ab124515, RRID:AB_2924667 Anti-F480 Abcam Cat# ab300421, RRID: AB_2936298 Flow cytometry antibodies list Table S5 N/A P62 Santa Cruz Cat# sc-10117, RRID: AB_2195900 LC3 Sigma Cat# L7543, RRID: AB_796155 ATGL Cell Signaling Cat# 2439, RRID: AB_2167953 PLIN Santa Cruz Biotechnology Cat# sc-67164, RRID: AB_2252681 HSL Cell Signaling Cat# 4107S, RIID: AB_2296900 Pyruvate Dehydrogenase E1 beta subunit antibody GeneTex Cat# GTX119625, RRID: AB_11163683 Beta Tubulin antibody Proteintech Cat# 10094-1-AP, RRID: AB_2210695 Beta Actin Polyclonal antibody Proteintech Cat# 20536-1-AP, RRID: AB_10700003 Anti-CD63 Antibody, System Biosciences System Biosciences Cat# EXOAB-CD63A-1, RRID: AB_2561274 Vinculin Monoclonal Antibody (VLN01) Thermo Fisher Scientific Cat# MA5-11690, RRID: AB_10976821 Bacterial and virus strains mitoDs-RED Addgene Plasmid #55838 RRID: Addgene_55838 Chemicals, peptides, and recombinant proteins Chloroquine diphosphate salt Sigma Aldrich #C6628 DNase I Sigma Aldrich Cat# 10104159001 3,30,5-Triiodo-L-thyronine sodium salt powder, BioReagent, suitable for cell culture Sigma Aldrich Cat# T6397 Rosiglitazone, R98% (HPLC) Sigma Aldrich Cat# R2408 Insulin solution human Sigma Aldrich Cat# I9278 Collagenase, Type I, powder Thermo Fisher Scientific Cat# 17100017 Collagenase, Type II, powder Thermo Fisher Scientific Cat# 17101015 eBioscienceTM 1X RBC Lysis Buffer Thermo Fisher Scientific Cat# 00-4333-57 3-Isobutyl-1-methylxanthine, BioUltra, R99% Sigma Aldrich Cat# I7018 Indomethacin Sigma Aldrich Cat# I7378 Cl 316,243 hydrate, R98% (HPLC), powder Sigma Aldrich Cat# C5976 Carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone, R98% (TLC), powder Sigma Aldrich Cat# C2920 N-Acetyl-L-cysteine, cell culture tested, BioReagent, CAS 616-91-1 Sigma Aldrich Cat# A9165 (Continued on next page) Cell Reports 43, 114447, July 23, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Doxycycline hyclate, R98% (HPLC) Sigma Aldrich Cat# D9891 Puromycin Invivogen Cat# ant-pr-1 Antimycin a from Streptomyces sp. Sigma Aldrich Cat# A8674 Lipopolysaccharides from Escherichia coli O111:B4, gamma-irradiated, BioXtra Sigma Aldrich Cat# L4391 LysoTracker red Thermo Fisher Scientific Cat# L12492 Mito Tracker Green Thermo Fisher Scientific Cat# M7514 MitoTrackerTM Red CMXRos Thermo Fisher Scientific Cat# M7512 BODIPY 493/503 Thermo Fisher Scientific Cat# D3922 Recombinant Mouse MCSF (Animal-Free) Cell Guidance Systems Cat# GMF8AF Critical commercial assays LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668019 OctoMACSTM Starting Kit Miltenyi Biotec Cat# 130-042-108 QuadroMACSTM Starting Kit (LS) Miltenyi Biotec Cat# 130-091-051 MS Columns Miltenyi Biotec Cat# 130-042-201 LS Columns Miltenyi Biotec Cat# 130-042-401 Pre-Separation Filters (30 mm) Miltenyi Biotec Cat# 130-041-407 RNeasy Lipid Tissue Mini Kit Qiagen Cat# 74804 Maxpar 10X Barcode Perm Buffer Fluidigm Cat# 201057 Cell-IDTM 20-Plex Pd Barcoding Kit Fluidigm Cat# 201060 Maxpar Cell Staining Buffer Fluidigm Cat# 201068 Cell-IDTM Intercalator-Ir Fluidigm Cat# 201192A EQ Four Element Calibration Beads Fluidigm Cat# 201078 Deposited data Single-Cell/RNAseq data (Gene Expression Omnibus) https://www.ncbi.nlm.nih.gov/geo/ GSE232278 PRoteomics IDEntification database (PRIDE) https://www.ebi.ac.uk/pride/ PXD042126 Experimental models: Cell lines T37i murine preadipocytes Professor Marc Lombes (INSERM U1185, Paris, France) N/A RAW 264.7 cell line ATCC Cat# TIB-71, RRID:CVCL_0493 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory #000664, RRID: IMS_JAX:000664 Ucp1D/D Gallerand et al.22 N/A MACsCD36KO Salk Institute for Biological Studies, La Jolla, CA, USA N/A db/db The Jackson Laboratory #000642, RIID: IMSR_JAX:000642 MitoFat Brestoff et al.23 N/A Oligonucleotides RT-qPCR Primer List Table S4 N/A Tgfb1 siRNA (mouse) Origene Cat# SR413084 Tgfb1 expression plasmid (mouse) Origene Cat# MR227339L1 Cd36 siRNA (mouse) Origene Cat# SR426922 Software and algorithms Desktop Wave Software Agilent Technologies N/A FunRich version 3.1.3 http://www.funrich.org N/A EnrichR https://amp.pharm.mssm.edu/Enrichr N/A (Continued on next page) 18 Cell Reports 43, 114447, July 23, 2024 ..



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