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mouse miltenyi biotec  (Miltenyi Biotec)


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    Miltenyi Biotec mouse miltenyi biotec
    Mouse Miltenyi Biotec, supplied by Miltenyi Biotec, used in various techniques. Bioz Stars score: 98/100, based on 2223 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/mouse+miltenyi/Tumor+Dissociation+Kit%2C+mouse/pm42531132-267-152-153
    Average 98 stars, based on 2223 article reviews
    mouse miltenyi biotec - by Bioz Stars, 2026-09
    98/100 stars

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    Related Articles

    Cream:

    Article Title: Autophagy maintains high endothelial venule identity and function during inflammation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti- Rat Ly6G (1A8) Biolegend Cat# 127601; RRID: AB_1089179 Fluorescein labeled Aleuria Aurantia Lectin Vector Labs VEC.FL-1391 RRID:AB_3752365 AF488 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A11034; RRID: AB_2576217 AF488 Donkey anti-Rat Secondary Antibody Invitrogen Cat# A21208; RRID: AB_2535794 AF488 Goat anti-Hamster Secondary Antibody Invitrogen Cat# A-21110; RRID: AB_2535759 AF647 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A21244; RRID: AB_2535812 AF488 Donkey anti-Rabbit Secondary Antibody Invitrogen Cat# A21206; RRID: AB_2535792 Anti-Rabbit CHST4 Aviva systems bio Cat# ARP35787_T100; RRID:AB_841312 Anti-Rabbit CD3 Novus Cat# NB600-1441; RRID: AB_789102 Anti-Goat CD31 R&D Biosystems Cat# AF3628; RRID: AB_2161028 Anti-Mouse LC3B Nanotools Cat# 0231-100; RRID: AB_2722733 Anti- F2-dylight633 Liu et al.29 N/A Mouse LTBR, Fc fusion HiPTM Recombinant Tebubio Cat# 71122; RRID:AB_3752369 Biological samples Human Tonsilitis sample 5686 This paper n/a Human Tonsilitis sample 5727 This paper n/a Human Tonsilitis sample 5730 This paper n/a Human Tonsilitis sample 5805 This paper n/a Human Tonsilitis sample 5823 This paper n/a Human Tonsilitis sample 5808 This paper n/a Human Tonsilitis sample 5804 This paper n/a Human Tonsilitis sample 5698 This paper n/a Human Psoriasis sample L1#79 This paper n/a Human Psoriasis sample L1#84 This paper n/a Human Psoriasis sample L1#90 This paper n/a Human Psoriasis sample L1#82 This paper n/a Human Psoriasis sample L1#66 This paper n/a Human Psoriasis sample L1#80 This paper n/a Human Psoriasis sample L1#68 This paper n/a Human Psoriasis sample L1#87 This paper n/a Other Bovine serum albumin (BSA) ThermoFisher Cat# 10270–106 RPMI Gibco Cat# 21875–034 Fetal bovine serum (FBS) SIgma Cat# B4287 L-Glutamine ThermoFisher Cat# 25030024 Phosphate buffered saline (PBS) ThermoFisher Cat# 14190094 Triton-100 Sigma Cat# T8787 Tween-20 Sigma-Merck Cat# P9416 Tamoxifen Sigma Cat# T5648 10% Neutral buffered formalin Sigma-Merck Cat# HT501128 TopVision Low Melting Point Agarose ThermoFisher Cat# R0801 7-AAD eBioscience Cat# 00-6993-50 Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-14 Fixable Viability Dye eFluor 450 eBioscience Cat# 65-0863-14 (Continued on next page) ll OPEN ACCESS Article e2 Immunity 59, 1–18.e1–e8, October 13, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase P Sigma/Merck Cat# 11213857001 DispaseII Sigma Cat# D4693-1G Dnase1 Worthington Cat# LS006333 4-Ethoxymethylene-2-phenyl-2oxazolin-5-one Sigma Cat# 862207 Aldara cream 5% MEDA N/A Critical commercial assays CD45 (TIL) MicroBeads, mouse Miltenyi Cat # 130-110-618 Click-iTTM Plus EdU Alexa FluorTM 647 Flow Cytometry Thermo scientific Cat# C10634 Depositied data Raw and processed scRNA-seq data (mouse) This paper GEO: GSE300153 Human tonsilitis data set De Martin et al. Biostudies Database: E-MTAB-11715 Mass spectrometry data (mouse) This paper Pride: PXD076099 Experimental models Mouse: Chst4-tdT reporter mice Hua et al.8 N/A Mouse: ATG12lox/lox x Chst4-Cre(ER)T2/ RFP mice This paper N/A Mouse: Ire1α lox/lox xChst4-Cre(ER)T2/ Tomato mice This paper N/A Mouse: CAG-RFP/EGFP/Map1lc3b)1Hill/J Li et al.22, Lin F et al.21 via JAX #027139 Mouse: ATG12 lox/lox Malhotra et al.58 N/A Mouse: ATG7 lox/lox Komatsu et al.59 N/A Mouse: C57BL/6NCrl Charles river Strain Code: 027 Mouse: Cdh5-CreER Sörensen et al.60 N/A Mouse: Ire1α lox/lox Zhang et al.61 N/A Mouse: Ltbr lox/lox Wimmer et al.62 N/A Software and algorithms R version 4.1.0 (2021-05-18) Platform: 386_64-w64-mingw32/364 (64-bit) Running under: Windows 10 3 64 (build 19041) R Core Team https://www.r-project.org Seurat_4.0.3 CRAN https://CRAN.R-project.org/ package=Seurat ggplot2_3.3.5 CRAN https://CRAN.R-project.org/ package=ggplot2 SeuratObject_4.0.2 CRAN https://CRAN.R-project.org/ package=SeuratObject ggpubr_0.4.0 CRAN https://CRAN.R-project.org/ package=ggpubr harmony_0.1.0 CRAN https://CRAN.R-project.org/ package=harmony AUCell_1.14.0 Bioconductor https://bioconductor.org/packages/AUCell GSVA_1.40.1 Bioconductor https:// bioconductor.org/packages/GSVA SeuratExtend_0.5.1 Hua et al.63 https://github.com/huayc09/ SeuratExtendSCENIC Nextflow pipeline Aibar S et al.64 https://github.com/aertslab/scenic-nf Python_3.8.3 Python http://www.python.org/ Palantir_0.2.6 Setty M et al.65 https://github.com/dpeerlab/Palantir Scvelo_0.2.2 Bergen V et al.66 https://scvelo.readthedocs.io/ Velocyto_0.17.17 La Manno G et al.67 http://velocyto.org/ (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–18.e1–e8, October 13, 2026 e3 ..

    Flow Cytometry:

    Article Title: Autophagy maintains high endothelial venule identity and function during inflammation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti- Rat Ly6G (1A8) Biolegend Cat# 127601; RRID: AB_1089179 Fluorescein labeled Aleuria Aurantia Lectin Vector Labs VEC.FL-1391 RRID:AB_3752365 AF488 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A11034; RRID: AB_2576217 AF488 Donkey anti-Rat Secondary Antibody Invitrogen Cat# A21208; RRID: AB_2535794 AF488 Goat anti-Hamster Secondary Antibody Invitrogen Cat# A-21110; RRID: AB_2535759 AF647 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A21244; RRID: AB_2535812 AF488 Donkey anti-Rabbit Secondary Antibody Invitrogen Cat# A21206; RRID: AB_2535792 Anti-Rabbit CHST4 Aviva systems bio Cat# ARP35787_T100; RRID:AB_841312 Anti-Rabbit CD3 Novus Cat# NB600-1441; RRID: AB_789102 Anti-Goat CD31 R&D Biosystems Cat# AF3628; RRID: AB_2161028 Anti-Mouse LC3B Nanotools Cat# 0231-100; RRID: AB_2722733 Anti- F2-dylight633 Liu et al.29 N/A Mouse LTBR, Fc fusion HiPTM Recombinant Tebubio Cat# 71122; RRID:AB_3752369 Biological samples Human Tonsilitis sample 5686 This paper n/a Human Tonsilitis sample 5727 This paper n/a Human Tonsilitis sample 5730 This paper n/a Human Tonsilitis sample 5805 This paper n/a Human Tonsilitis sample 5823 This paper n/a Human Tonsilitis sample 5808 This paper n/a Human Tonsilitis sample 5804 This paper n/a Human Tonsilitis sample 5698 This paper n/a Human Psoriasis sample L1#79 This paper n/a Human Psoriasis sample L1#84 This paper n/a Human Psoriasis sample L1#90 This paper n/a Human Psoriasis sample L1#82 This paper n/a Human Psoriasis sample L1#66 This paper n/a Human Psoriasis sample L1#80 This paper n/a Human Psoriasis sample L1#68 This paper n/a Human Psoriasis sample L1#87 This paper n/a Other Bovine serum albumin (BSA) ThermoFisher Cat# 10270–106 RPMI Gibco Cat# 21875–034 Fetal bovine serum (FBS) SIgma Cat# B4287 L-Glutamine ThermoFisher Cat# 25030024 Phosphate buffered saline (PBS) ThermoFisher Cat# 14190094 Triton-100 Sigma Cat# T8787 Tween-20 Sigma-Merck Cat# P9416 Tamoxifen Sigma Cat# T5648 10% Neutral buffered formalin Sigma-Merck Cat# HT501128 TopVision Low Melting Point Agarose ThermoFisher Cat# R0801 7-AAD eBioscience Cat# 00-6993-50 Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-14 Fixable Viability Dye eFluor 450 eBioscience Cat# 65-0863-14 (Continued on next page) ll OPEN ACCESS Article e2 Immunity 59, 1–18.e1–e8, October 13, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase P Sigma/Merck Cat# 11213857001 DispaseII Sigma Cat# D4693-1G Dnase1 Worthington Cat# LS006333 4-Ethoxymethylene-2-phenyl-2oxazolin-5-one Sigma Cat# 862207 Aldara cream 5% MEDA N/A Critical commercial assays CD45 (TIL) MicroBeads, mouse Miltenyi Cat # 130-110-618 Click-iTTM Plus EdU Alexa FluorTM 647 Flow Cytometry Thermo scientific Cat# C10634 Depositied data Raw and processed scRNA-seq data (mouse) This paper GEO: GSE300153 Human tonsilitis data set De Martin et al. Biostudies Database: E-MTAB-11715 Mass spectrometry data (mouse) This paper Pride: PXD076099 Experimental models Mouse: Chst4-tdT reporter mice Hua et al.8 N/A Mouse: ATG12lox/lox x Chst4-Cre(ER)T2/ RFP mice This paper N/A Mouse: Ire1α lox/lox xChst4-Cre(ER)T2/ Tomato mice This paper N/A Mouse: CAG-RFP/EGFP/Map1lc3b)1Hill/J Li et al.22, Lin F et al.21 via JAX #027139 Mouse: ATG12 lox/lox Malhotra et al.58 N/A Mouse: ATG7 lox/lox Komatsu et al.59 N/A Mouse: C57BL/6NCrl Charles river Strain Code: 027 Mouse: Cdh5-CreER Sörensen et al.60 N/A Mouse: Ire1α lox/lox Zhang et al.61 N/A Mouse: Ltbr lox/lox Wimmer et al.62 N/A Software and algorithms R version 4.1.0 (2021-05-18) Platform: 386_64-w64-mingw32/364 (64-bit) Running under: Windows 10 3 64 (build 19041) R Core Team https://www.r-project.org Seurat_4.0.3 CRAN https://CRAN.R-project.org/ package=Seurat ggplot2_3.3.5 CRAN https://CRAN.R-project.org/ package=ggplot2 SeuratObject_4.0.2 CRAN https://CRAN.R-project.org/ package=SeuratObject ggpubr_0.4.0 CRAN https://CRAN.R-project.org/ package=ggpubr harmony_0.1.0 CRAN https://CRAN.R-project.org/ package=harmony AUCell_1.14.0 Bioconductor https://bioconductor.org/packages/AUCell GSVA_1.40.1 Bioconductor https:// bioconductor.org/packages/GSVA SeuratExtend_0.5.1 Hua et al.63 https://github.com/huayc09/ SeuratExtendSCENIC Nextflow pipeline Aibar S et al.64 https://github.com/aertslab/scenic-nf Python_3.8.3 Python http://www.python.org/ Palantir_0.2.6 Setty M et al.65 https://github.com/dpeerlab/Palantir Scvelo_0.2.2 Bergen V et al.66 https://scvelo.readthedocs.io/ Velocyto_0.17.17 La Manno G et al.67 http://velocyto.org/ (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–18.e1–e8, October 13, 2026 e3 ..

    Mass Spectrometry:

    Article Title: Autophagy maintains high endothelial venule identity and function during inflammation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti- Rat Ly6G (1A8) Biolegend Cat# 127601; RRID: AB_1089179 Fluorescein labeled Aleuria Aurantia Lectin Vector Labs VEC.FL-1391 RRID:AB_3752365 AF488 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A11034; RRID: AB_2576217 AF488 Donkey anti-Rat Secondary Antibody Invitrogen Cat# A21208; RRID: AB_2535794 AF488 Goat anti-Hamster Secondary Antibody Invitrogen Cat# A-21110; RRID: AB_2535759 AF647 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A21244; RRID: AB_2535812 AF488 Donkey anti-Rabbit Secondary Antibody Invitrogen Cat# A21206; RRID: AB_2535792 Anti-Rabbit CHST4 Aviva systems bio Cat# ARP35787_T100; RRID:AB_841312 Anti-Rabbit CD3 Novus Cat# NB600-1441; RRID: AB_789102 Anti-Goat CD31 R&D Biosystems Cat# AF3628; RRID: AB_2161028 Anti-Mouse LC3B Nanotools Cat# 0231-100; RRID: AB_2722733 Anti- F2-dylight633 Liu et al.29 N/A Mouse LTBR, Fc fusion HiPTM Recombinant Tebubio Cat# 71122; RRID:AB_3752369 Biological samples Human Tonsilitis sample 5686 This paper n/a Human Tonsilitis sample 5727 This paper n/a Human Tonsilitis sample 5730 This paper n/a Human Tonsilitis sample 5805 This paper n/a Human Tonsilitis sample 5823 This paper n/a Human Tonsilitis sample 5808 This paper n/a Human Tonsilitis sample 5804 This paper n/a Human Tonsilitis sample 5698 This paper n/a Human Psoriasis sample L1#79 This paper n/a Human Psoriasis sample L1#84 This paper n/a Human Psoriasis sample L1#90 This paper n/a Human Psoriasis sample L1#82 This paper n/a Human Psoriasis sample L1#66 This paper n/a Human Psoriasis sample L1#80 This paper n/a Human Psoriasis sample L1#68 This paper n/a Human Psoriasis sample L1#87 This paper n/a Other Bovine serum albumin (BSA) ThermoFisher Cat# 10270–106 RPMI Gibco Cat# 21875–034 Fetal bovine serum (FBS) SIgma Cat# B4287 L-Glutamine ThermoFisher Cat# 25030024 Phosphate buffered saline (PBS) ThermoFisher Cat# 14190094 Triton-100 Sigma Cat# T8787 Tween-20 Sigma-Merck Cat# P9416 Tamoxifen Sigma Cat# T5648 10% Neutral buffered formalin Sigma-Merck Cat# HT501128 TopVision Low Melting Point Agarose ThermoFisher Cat# R0801 7-AAD eBioscience Cat# 00-6993-50 Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-14 Fixable Viability Dye eFluor 450 eBioscience Cat# 65-0863-14 (Continued on next page) ll OPEN ACCESS Article e2 Immunity 59, 1–18.e1–e8, October 13, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase P Sigma/Merck Cat# 11213857001 DispaseII Sigma Cat# D4693-1G Dnase1 Worthington Cat# LS006333 4-Ethoxymethylene-2-phenyl-2oxazolin-5-one Sigma Cat# 862207 Aldara cream 5% MEDA N/A Critical commercial assays CD45 (TIL) MicroBeads, mouse Miltenyi Cat # 130-110-618 Click-iTTM Plus EdU Alexa FluorTM 647 Flow Cytometry Thermo scientific Cat# C10634 Depositied data Raw and processed scRNA-seq data (mouse) This paper GEO: GSE300153 Human tonsilitis data set De Martin et al. Biostudies Database: E-MTAB-11715 Mass spectrometry data (mouse) This paper Pride: PXD076099 Experimental models Mouse: Chst4-tdT reporter mice Hua et al.8 N/A Mouse: ATG12lox/lox x Chst4-Cre(ER)T2/ RFP mice This paper N/A Mouse: Ire1α lox/lox xChst4-Cre(ER)T2/ Tomato mice This paper N/A Mouse: CAG-RFP/EGFP/Map1lc3b)1Hill/J Li et al.22, Lin F et al.21 via JAX #027139 Mouse: ATG12 lox/lox Malhotra et al.58 N/A Mouse: ATG7 lox/lox Komatsu et al.59 N/A Mouse: C57BL/6NCrl Charles river Strain Code: 027 Mouse: Cdh5-CreER Sörensen et al.60 N/A Mouse: Ire1α lox/lox Zhang et al.61 N/A Mouse: Ltbr lox/lox Wimmer et al.62 N/A Software and algorithms R version 4.1.0 (2021-05-18) Platform: 386_64-w64-mingw32/364 (64-bit) Running under: Windows 10 3 64 (build 19041) R Core Team https://www.r-project.org Seurat_4.0.3 CRAN https://CRAN.R-project.org/ package=Seurat ggplot2_3.3.5 CRAN https://CRAN.R-project.org/ package=ggplot2 SeuratObject_4.0.2 CRAN https://CRAN.R-project.org/ package=SeuratObject ggpubr_0.4.0 CRAN https://CRAN.R-project.org/ package=ggpubr harmony_0.1.0 CRAN https://CRAN.R-project.org/ package=harmony AUCell_1.14.0 Bioconductor https://bioconductor.org/packages/AUCell GSVA_1.40.1 Bioconductor https:// bioconductor.org/packages/GSVA SeuratExtend_0.5.1 Hua et al.63 https://github.com/huayc09/ SeuratExtendSCENIC Nextflow pipeline Aibar S et al.64 https://github.com/aertslab/scenic-nf Python_3.8.3 Python http://www.python.org/ Palantir_0.2.6 Setty M et al.65 https://github.com/dpeerlab/Palantir Scvelo_0.2.2 Bergen V et al.66 https://scvelo.readthedocs.io/ Velocyto_0.17.17 La Manno G et al.67 http://velocyto.org/ (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–18.e1–e8, October 13, 2026 e3 ..

    Software:

    Article Title: Autophagy maintains high endothelial venule identity and function during inflammation.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Anti- Rat Ly6G (1A8) Biolegend Cat# 127601; RRID: AB_1089179 Fluorescein labeled Aleuria Aurantia Lectin Vector Labs VEC.FL-1391 RRID:AB_3752365 AF488 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A11034; RRID: AB_2576217 AF488 Donkey anti-Rat Secondary Antibody Invitrogen Cat# A21208; RRID: AB_2535794 AF488 Goat anti-Hamster Secondary Antibody Invitrogen Cat# A-21110; RRID: AB_2535759 AF647 Goat anti-Rabbit Secondary Antibody Invitrogen Cat# A21244; RRID: AB_2535812 AF488 Donkey anti-Rabbit Secondary Antibody Invitrogen Cat# A21206; RRID: AB_2535792 Anti-Rabbit CHST4 Aviva systems bio Cat# ARP35787_T100; RRID:AB_841312 Anti-Rabbit CD3 Novus Cat# NB600-1441; RRID: AB_789102 Anti-Goat CD31 R&D Biosystems Cat# AF3628; RRID: AB_2161028 Anti-Mouse LC3B Nanotools Cat# 0231-100; RRID: AB_2722733 Anti- F2-dylight633 Liu et al.29 N/A Mouse LTBR, Fc fusion HiPTM Recombinant Tebubio Cat# 71122; RRID:AB_3752369 Biological samples Human Tonsilitis sample 5686 This paper n/a Human Tonsilitis sample 5727 This paper n/a Human Tonsilitis sample 5730 This paper n/a Human Tonsilitis sample 5805 This paper n/a Human Tonsilitis sample 5823 This paper n/a Human Tonsilitis sample 5808 This paper n/a Human Tonsilitis sample 5804 This paper n/a Human Tonsilitis sample 5698 This paper n/a Human Psoriasis sample L1#79 This paper n/a Human Psoriasis sample L1#84 This paper n/a Human Psoriasis sample L1#90 This paper n/a Human Psoriasis sample L1#82 This paper n/a Human Psoriasis sample L1#66 This paper n/a Human Psoriasis sample L1#80 This paper n/a Human Psoriasis sample L1#68 This paper n/a Human Psoriasis sample L1#87 This paper n/a Other Bovine serum albumin (BSA) ThermoFisher Cat# 10270–106 RPMI Gibco Cat# 21875–034 Fetal bovine serum (FBS) SIgma Cat# B4287 L-Glutamine ThermoFisher Cat# 25030024 Phosphate buffered saline (PBS) ThermoFisher Cat# 14190094 Triton-100 Sigma Cat# T8787 Tween-20 Sigma-Merck Cat# P9416 Tamoxifen Sigma Cat# T5648 10% Neutral buffered formalin Sigma-Merck Cat# HT501128 TopVision Low Melting Point Agarose ThermoFisher Cat# R0801 7-AAD eBioscience Cat# 00-6993-50 Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-14 Fixable Viability Dye eFluor 450 eBioscience Cat# 65-0863-14 (Continued on next page) ll OPEN ACCESS Article e2 Immunity 59, 1–18.e1–e8, October 13, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Collagenase P Sigma/Merck Cat# 11213857001 DispaseII Sigma Cat# D4693-1G Dnase1 Worthington Cat# LS006333 4-Ethoxymethylene-2-phenyl-2oxazolin-5-one Sigma Cat# 862207 Aldara cream 5% MEDA N/A Critical commercial assays CD45 (TIL) MicroBeads, mouse Miltenyi Cat # 130-110-618 Click-iTTM Plus EdU Alexa FluorTM 647 Flow Cytometry Thermo scientific Cat# C10634 Depositied data Raw and processed scRNA-seq data (mouse) This paper GEO: GSE300153 Human tonsilitis data set De Martin et al. Biostudies Database: E-MTAB-11715 Mass spectrometry data (mouse) This paper Pride: PXD076099 Experimental models Mouse: Chst4-tdT reporter mice Hua et al.8 N/A Mouse: ATG12lox/lox x Chst4-Cre(ER)T2/ RFP mice This paper N/A Mouse: Ire1α lox/lox xChst4-Cre(ER)T2/ Tomato mice This paper N/A Mouse: CAG-RFP/EGFP/Map1lc3b)1Hill/J Li et al.22, Lin F et al.21 via JAX #027139 Mouse: ATG12 lox/lox Malhotra et al.58 N/A Mouse: ATG7 lox/lox Komatsu et al.59 N/A Mouse: C57BL/6NCrl Charles river Strain Code: 027 Mouse: Cdh5-CreER Sörensen et al.60 N/A Mouse: Ire1α lox/lox Zhang et al.61 N/A Mouse: Ltbr lox/lox Wimmer et al.62 N/A Software and algorithms R version 4.1.0 (2021-05-18) Platform: 386_64-w64-mingw32/364 (64-bit) Running under: Windows 10 3 64 (build 19041) R Core Team https://www.r-project.org Seurat_4.0.3 CRAN https://CRAN.R-project.org/ package=Seurat ggplot2_3.3.5 CRAN https://CRAN.R-project.org/ package=ggplot2 SeuratObject_4.0.2 CRAN https://CRAN.R-project.org/ package=SeuratObject ggpubr_0.4.0 CRAN https://CRAN.R-project.org/ package=ggpubr harmony_0.1.0 CRAN https://CRAN.R-project.org/ package=harmony AUCell_1.14.0 Bioconductor https://bioconductor.org/packages/AUCell GSVA_1.40.1 Bioconductor https:// bioconductor.org/packages/GSVA SeuratExtend_0.5.1 Hua et al.63 https://github.com/huayc09/ SeuratExtendSCENIC Nextflow pipeline Aibar S et al.64 https://github.com/aertslab/scenic-nf Python_3.8.3 Python http://www.python.org/ Palantir_0.2.6 Setty M et al.65 https://github.com/dpeerlab/Palantir Scvelo_0.2.2 Bergen V et al.66 https://scvelo.readthedocs.io/ Velocyto_0.17.17 La Manno G et al.67 http://velocyto.org/ (Continued on next page) ll OPEN ACCESSArticle Immunity 59, 1–18.e1–e8, October 13, 2026 e3 ..

    Synthesized:

    Article Title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development.
    Article Snippet: Article Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development

    Reverse Transcription:

    Article Title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development.
    Article Snippet: Article Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development

    Enzyme-linked Immunosorbent Assay:

    Article Title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development.
    Article Snippet: Article Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development

    AST Assay:

    Article Title: Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development.
    Article Snippet: Article Tumor-associated Schwann cell remodeling under metabolic stress via lactate sensing orchestrates pancreatic ductal adenocarcinoma development

    Staining:

    Article Title: Optimization of Erythrocyte Lysis Protocols for Robust and Reproducible T Cell Analysis in Murine Peripheral Blood, Spleen, Lung, and Bone Marrow.
    Article Snippet: .. Antigen Clone Fluorochrome Dilution Surface/intracellular Fixable Viability Stain 620 — FVS620 1:1000 Surface Ghost Dye Violet 540 fixable viability dye — Violet 540 1:5000 Surface CD45 30-F11 PE-Cy7 3:1000 Surface CD3 17A2 BV510 1:200 Surface CD3 17A2 FITC 1:500 Surface CD4 RM4-5 APC 1:800 Surface CD4 GK1.5 PE/Dazzle 594 1:800 Surface CD8a 53-6.7 FITC 1:500 Surface CD8a 53-6.7 APC 1:800 Surface Ghost Dye Violet 540 fixable viability dye TONBO Cat#72086 Anti-CD45 antibody BD Cat#552848 Anti-CD3 antibody BioLegend Cat#100234 Anti-CD3 antibody BioLegend Cat#100204 Anti-CD4 antibody BD Cat#553051 Anti-CD4 antibody BioLegend Cat#100456 Anti-CD8a antibody BioLegend Cat#100706 Anti-CD8a antibody BioLegend Cat#100712 Lysing solution 10x concentrate BD Cat#349202 RBC lysis buffer (10x) BioLegend Cat#420301 Red blood cell lysis buffer Biosharp Cat#BL503B 3% acetic acid with methylene blue Stemcell Cat#07060 Fetal bovine serum (FBS) ExCell Cat#FSP500 Albumin from bovine serum Macklin Cat#B917420-200g Phosphate-buffer saline (PBS) Solarbio Cat#G0002 MACS tissue storage solution Miltenyi Cat#130-100-008 Lung dissociation kit, mouse Miltenyi Cat130-095-927 gentleMACS 25C Tubes C Miltenyi Cat#130-093-237 70 μm cell strainers Biosharp Cat#BS-70-XBS-N1 Heparin sodium anticoagulant tube 1.5mL Solarbio Cat#YA1471 Isoflurane anesthetic RWD Cat#R510-22-10 4 of 19 Journal of Immunology Research, 2026 1607, 2026, 1, D ow nloaded from https://onlinelibrary.w iley.com /doi/10.1155/jim r/3335332 by IN A SP - N E PA L , W iley O nline L ibrary on [10/04/2026]. ..

    Article Title: The transcription factor Helios restrains the anti-tumor capacity of CD8 + T cells.
    Article Snippet: Cas9 Nuclease V3 IDT Cat#1081058 Blasticidin S HCl Invitrogen Cat#R21001 ALV2 MedChemExpress Cat#HY-137206 BNTX maleate Abcam Cat#AB146142 KF 38789 Tocris Bioscience Cat#2748 SUN-B 8155 Tocris Bioscience Cat#2550 Adapalene Merck Cat#A7486 Ghost Dye Red 780 Tonbo Biosciences Cat#13-0865 Ghost Dye Red 710 Tonbo Biosciences Cat#13-0871 (Continued on next page) Cell Reports 44, 116680, December 23, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SYTOXTM Orange Dead Cell Stain Invitrogen Cat#S34861 Annexin V-APC Tonbo Biosciences Cat#20-6409 Annexin V Binding Buffer Tonbo Biosciences Cat#TNB-5000 Critical commercial assays Foxp3/Transcription Factor Stainning Buffer Kit Tonbo Biosciences Cat#TNB-0607 BD Cytofix/Cytoperm Plus BD Biosciences Cat#555028 TrueTagTM DNA Donor Kit Thermo Fisher Scientific Cat#A42992 Neon NxT Electroporation System Invitrogen Cat#NEON1S CD8a+ T cell Isolation Kit, mouse Miltenyi Cat130-104-075 ATAC-Seq Kit Active Motif Cat#53150 CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat#C34557 Deposited data scRNA-seq/ATAC-seq PRJEB101308 ENA (EMBL-EBI) Experimental models: Cell lines Jurkat E6.1 ATCC RRID:CVCL_0367 .. MC38 Gift from Dr. Santos Mañés, Centro Nacional de Biotecnologı́a/CSIC, Spain RRID:CVCL_B288 B16-F10 Gift from Dr. Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico RRID:CVCL_F936 B16-F10OVA Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A HTB-176 Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664; RRID:IMSR_JAX:000664 Mouse: C57BL/6-Tg(Cd8a-cre)1Itan/J The Jackson Laboratory Cat#008766; RRID:IMSR_JAX:008766 Mouse: B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ The Jackson Laboratory Cat#022071; RRID:IMSR_JAX:022071 Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory Cat#003831; RRID:IMSR_JAX:003831 Mouse: C57BL/6-Tg(CAG-OVAL)916Jen/J The Jackson Laboratory Cat#005145; RRID:IMSR_JAX:005145 Mouse: B6.129S7-Rag1tm1Mom/J The Jackson Laboratory Cat#002216; RRID:IMSR_JAX:002216 Mouse: PD-1− /− Gift from Dr. Arlene H. Sharpe (Harvard Medical School) N/A Mouse: Ikzf2-flox/flox Gift from Dr. Angela Thornton (NIAID) N/A Software and algorithms GraphPad Prism 10.1 GraphPad RRID: SCR_002798 http://www.graphpad.com/ NovoExpress Agilent RRID: SCR_024676 ImageJ NIH https://rsbweb.nih.gov/ij/ Cellpose 2.0 Ref. 64 RRID:SCR_021716; http://www.cellpose.org/ r-tidyverse R/Anaconda https://anaconda.org/conda-forge/r-tidyverse r-dplyr R/Anaconda https://anaconda.org/conda-forge/r-dplyr r-data.table R/Anaconda https://anaconda.org/conda-forge/r-data.table r-ggplot2 R/Anaconda https://anaconda.org/conda-forge/r-ggplot2 r-ggpubr R/Anaconda https://anaconda.org/conda-forge/r-ggpubr MiXCR Ref. 59 https://github.com/milaboratory/mixcr fastqc Anaconda https://anaconda.org/bioconda/fastqc trim-galore Anaconda https://anaconda.org/bioconda/trim-galore samtools Anaconda https://anaconda.org/bioconda/samtools (Continued on next page) 18 Cell Reports 44, 116680, December 23, 2025

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Article Title: Innate lymphoid cells integrate sensing and plasticity to control fungal infections
    Article Snippet: Cat# 65-0840-90 Cyanine5 Streptavidin Biolegend Cat#405209 APC-Fire750 Streptavidin Biolegend Cat#405250 Streptavidin-DyLight 488 (currently marketed as Alexa Fluor 488) Jackson ImmunoResearch Cat#016-540-084 7-AAD Viability Staining Solution Biolegend Cat#420403 Apotracker Green Biolegend Cat#427401 Zombie Aqua Fixable Viability Kit Biolegend Cat#423102 Zombie NIR Fixable Viability Kit Biolegend Cat#423105 Zombie Violet Fixable Viability Kit Biolegend Cat#423113 Collagenase II Gibco; Fisher Scientific Cat# 17101015 DNAse I Sigma-Aldrich Cat#10104159001 Percoll GE-Healthcare Cat#GE17-0891-01 Recombinant Mouse IL-2 Biolegend Cat#575404 Recombinant Mouse IL-7 Biolegend Cat#577802 Recombinant Mouse SCF Miltenyi Cat#130-101-693 Recombinant Mouse IL-1β MedchemExpress Cat# MCE-HY-P7073A-2μg Recombinant Mouse IL-23 Biolegend Cat#589002 Recombinant Mouse IL-17C BioTechne Cat#2306-ML-025 Recombinant Rat/Mouse TGFβ1 MedchemExpress MCE-HY-P7117-2μg Brefeldin A Biolegend Cat#420601 Phorbol myristate acetate (PMA) Sigma-Aldrich Cat#P1585 Ionomycin Sigma-Aldrich Cat#IO634 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D2438 Zymosan Sigma-Aldrich Cat#Z4250 Curdlan Invivogen Cat#tlrl-cura Laminarin Invivogen Cat#tlrl-lam Chitin Wagener et al.115 N/A Dynasore hydrate Sigma-Aldrich Cat#D7693 R406 (Syk Inhibitor) Selleckchem Cat#S2194 α-D-Mannan Sigma-Aldrich Cat#M7504 Ketamin: Ketasol Livisto GTIN# 04050478000336 Xylazine: Sedaxylan Dechra GTIN# 08714225157464 Intracellular Staining Permeabilization Wash Buffer (10X) Biolegend Cat#421002 Fixation Buffer Biolegend Cat#420801 (Continued on next page) 22 Cell Reports 45, 117140, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Red Blood Cell Lysis Buffer (10X) Biolegend Cat#420302 True-Phos Perm Buffer Biolegend Cat#425401 Dulbecco’s Phosphate Buffered Saline Sigma-Aldrich Cat#8537 Hanks’ Balanced Salt solution Sigma-Aldrich Cat#8264 IMDM (Iscove’s Modified Dulbecco’s Medium) Lonza Cat#12-722F RPMI 1640 Medium Gibco; Fisher Scientific Cat#21875091 GlutaMAX Supplement Gibco; Fisher Scientific Cat#35050061 HEPES (1M) Gibco; Fisher Scientific Cat#15630080 Sodium pyruvate solution,100 mM Sigma-Aldrich Cat#S8636 MEM Non-essential Amino Acid Solution (100X) Sigma-Aldrich Cat#M7145 RNAlater Sigma-Aldrich Cat#R0901 z-IETD-FMK MedchemExpress Cat#MCE-HY-101297-1mg Necrostatin-1 MedchemExpress Cat#HY-15760 Ultra PureTM Distilled DNAse/RNAse free Water Invitrogen; Fisher Scientific Cat#10977049 Commercial assays Lineage cell depletion kit, mouse Miltenyi Cat130-090-858 Foxp3/Transcription Factor Staining Buffer Set-1 kit eBioscience, Fisher Scient. .. Cat#00-5523-00 System for Reverse Transcription Using AMV RT Promega Cat#A3500 SsoAdvanced Universal SYBR Green Supermix Biorad Cat#1725271 QIAGEN RNeasy Plus Micro Kit Quiagen Cat#74034 Monarch Spin RNA Cleanup Kit (10 μg) New England Biolabs Cat#T2030L Deposited data Mass Spectrometry of culture supernatants (ILC-Cgl interaction) ProteomeXchange Consortium111 PRIDE:PXD061271 Pulmonary ILC Sequencing (Smart-Seq2) GEO-database GEO:GSE293220 RNA-Sequencing of infected lung tissues after ILC-transfer GEO-database GEO:GSE293054 Experimental models cell lines Feeder cells: OP9-DL1 Gift of Meinrad Busslinger Schmitt & Zúñiga-Pflücker116 Experimental murine models, strains Mouse: C57BL/6J mice Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000664 Mouse: Rag1− /− : B6.129S7-Rag1tm1Mom/J Jackson Laboratory RRID:IMSR_JAX:002096 Mouse: Rag2− /− Il2rg− /− Cao et al.117 Veronika Sexl Mouse: IL17A-IRES-GFP-KI reporter: C57BL/6-Il17atm1Bcgen/J Jackson Laboratory RRID: IMSR_JAX:018472 Mouse: Tec− /− Rag1− /− IL-17AeGFP: C57BL/6Il17atm1Bcgen/J x Tectm1Welm x B6.129S7-Rag1tm1Mom/J This study N/A Mouse: Dectin-1− /− : B6.129S6-Clec7atm1Gdb/J Taylor et al.118 RRID:IMSR_JAX:012337 Mouse: Dectin-2− /− : Clec4ntm1Yiw Saijo et al.119 MGI:4459637 Mouse: Tlr2/− : Tlr2tm1Aki Takeuchi et al.120 MGI:2178675 Mouse: Tlr4− /− : Tlr4tm1Aki Hashino et al.121 MGI:1860885 Mouse: Tec− /− : Tectm1Welm Ellmeier et al.34 MGI:2450883 Oligonucleotides m-Eef1a forward/reverse (5′-3′): ACGAGGCAATGTTG CTGGTGAC/GTGTGACAATCCAGAACAGGAGC Origene Cat#MP204369; GenBank:NM_010106 m-Tgfb1 forward/reverse (5′-3′): TGACGTCACTGGA GTTGTACGG/GGTTCATGTCATGGATGGTGC N/A GenBank:NM_011577.2 m-Il1b forward/reverse (5′-3′): (CCAACAAGTGATAT TCTCCATGAG/TCTTTCATTACACAGGACAGGT) N/A GenBank:NM_008361.4 (Continued on next page) Cell Reports 45, 117140, April 28, 2026 23

    Red Blood Cell Lysis:

    Article Title: Optimization of Erythrocyte Lysis Protocols for Robust and Reproducible T Cell Analysis in Murine Peripheral Blood, Spleen, Lung, and Bone Marrow.
    Article Snippet: .. Antigen Clone Fluorochrome Dilution Surface/intracellular Fixable Viability Stain 620 — FVS620 1:1000 Surface Ghost Dye Violet 540 fixable viability dye — Violet 540 1:5000 Surface CD45 30-F11 PE-Cy7 3:1000 Surface CD3 17A2 BV510 1:200 Surface CD3 17A2 FITC 1:500 Surface CD4 RM4-5 APC 1:800 Surface CD4 GK1.5 PE/Dazzle 594 1:800 Surface CD8a 53-6.7 FITC 1:500 Surface CD8a 53-6.7 APC 1:800 Surface Ghost Dye Violet 540 fixable viability dye TONBO Cat#72086 Anti-CD45 antibody BD Cat#552848 Anti-CD3 antibody BioLegend Cat#100234 Anti-CD3 antibody BioLegend Cat#100204 Anti-CD4 antibody BD Cat#553051 Anti-CD4 antibody BioLegend Cat#100456 Anti-CD8a antibody BioLegend Cat#100706 Anti-CD8a antibody BioLegend Cat#100712 Lysing solution 10x concentrate BD Cat#349202 RBC lysis buffer (10x) BioLegend Cat#420301 Red blood cell lysis buffer Biosharp Cat#BL503B 3% acetic acid with methylene blue Stemcell Cat#07060 Fetal bovine serum (FBS) ExCell Cat#FSP500 Albumin from bovine serum Macklin Cat#B917420-200g Phosphate-buffer saline (PBS) Solarbio Cat#G0002 MACS tissue storage solution Miltenyi Cat#130-100-008 Lung dissociation kit, mouse Miltenyi Cat130-095-927 gentleMACS 25C Tubes C Miltenyi Cat#130-093-237 70 μm cell strainers Biosharp Cat#BS-70-XBS-N1 Heparin sodium anticoagulant tube 1.5mL Solarbio Cat#YA1471 Isoflurane anesthetic RWD Cat#R510-22-10 4 of 19 Journal of Immunology Research, 2026 1607, 2026, 1, D ow nloaded from https://onlinelibrary.w iley.com /doi/10.1155/jim r/3335332 by IN A SP - N E PA L , W iley O nline L ibrary on [10/04/2026]. ..

    Article Title: Innate lymphoid cells integrate sensing and plasticity to control fungal infections
    Article Snippet: Cat# 65-0840-90 Cyanine5 Streptavidin Biolegend Cat#405209 APC-Fire750 Streptavidin Biolegend Cat#405250 Streptavidin-DyLight 488 (currently marketed as Alexa Fluor 488) Jackson ImmunoResearch Cat#016-540-084 7-AAD Viability Staining Solution Biolegend Cat#420403 Apotracker Green Biolegend Cat#427401 Zombie Aqua Fixable Viability Kit Biolegend Cat#423102 Zombie NIR Fixable Viability Kit Biolegend Cat#423105 Zombie Violet Fixable Viability Kit Biolegend Cat#423113 Collagenase II Gibco; Fisher Scientific Cat# 17101015 DNAse I Sigma-Aldrich Cat#10104159001 Percoll GE-Healthcare Cat#GE17-0891-01 Recombinant Mouse IL-2 Biolegend Cat#575404 Recombinant Mouse IL-7 Biolegend Cat#577802 Recombinant Mouse SCF Miltenyi Cat#130-101-693 Recombinant Mouse IL-1β MedchemExpress Cat# MCE-HY-P7073A-2μg Recombinant Mouse IL-23 Biolegend Cat#589002 Recombinant Mouse IL-17C BioTechne Cat#2306-ML-025 Recombinant Rat/Mouse TGFβ1 MedchemExpress MCE-HY-P7117-2μg Brefeldin A Biolegend Cat#420601 Phorbol myristate acetate (PMA) Sigma-Aldrich Cat#P1585 Ionomycin Sigma-Aldrich Cat#IO634 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D2438 Zymosan Sigma-Aldrich Cat#Z4250 Curdlan Invivogen Cat#tlrl-cura Laminarin Invivogen Cat#tlrl-lam Chitin Wagener et al.115 N/A Dynasore hydrate Sigma-Aldrich Cat#D7693 R406 (Syk Inhibitor) Selleckchem Cat#S2194 α-D-Mannan Sigma-Aldrich Cat#M7504 Ketamin: Ketasol Livisto GTIN# 04050478000336 Xylazine: Sedaxylan Dechra GTIN# 08714225157464 Intracellular Staining Permeabilization Wash Buffer (10X) Biolegend Cat#421002 Fixation Buffer Biolegend Cat#420801 (Continued on next page) 22 Cell Reports 45, 117140, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Red Blood Cell Lysis Buffer (10X) Biolegend Cat#420302 True-Phos Perm Buffer Biolegend Cat#425401 Dulbecco’s Phosphate Buffered Saline Sigma-Aldrich Cat#8537 Hanks’ Balanced Salt solution Sigma-Aldrich Cat#8264 IMDM (Iscove’s Modified Dulbecco’s Medium) Lonza Cat#12-722F RPMI 1640 Medium Gibco; Fisher Scientific Cat#21875091 GlutaMAX Supplement Gibco; Fisher Scientific Cat#35050061 HEPES (1M) Gibco; Fisher Scientific Cat#15630080 Sodium pyruvate solution,100 mM Sigma-Aldrich Cat#S8636 MEM Non-essential Amino Acid Solution (100X) Sigma-Aldrich Cat#M7145 RNAlater Sigma-Aldrich Cat#R0901 z-IETD-FMK MedchemExpress Cat#MCE-HY-101297-1mg Necrostatin-1 MedchemExpress Cat#HY-15760 Ultra PureTM Distilled DNAse/RNAse free Water Invitrogen; Fisher Scientific Cat#10977049 Commercial assays Lineage cell depletion kit, mouse Miltenyi Cat130-090-858 Foxp3/Transcription Factor Staining Buffer Set-1 kit eBioscience, Fisher Scient. .. Cat#00-5523-00 System for Reverse Transcription Using AMV RT Promega Cat#A3500 SsoAdvanced Universal SYBR Green Supermix Biorad Cat#1725271 QIAGEN RNeasy Plus Micro Kit Quiagen Cat#74034 Monarch Spin RNA Cleanup Kit (10 μg) New England Biolabs Cat#T2030L Deposited data Mass Spectrometry of culture supernatants (ILC-Cgl interaction) ProteomeXchange Consortium111 PRIDE:PXD061271 Pulmonary ILC Sequencing (Smart-Seq2) GEO-database GEO:GSE293220 RNA-Sequencing of infected lung tissues after ILC-transfer GEO-database GEO:GSE293054 Experimental models cell lines Feeder cells: OP9-DL1 Gift of Meinrad Busslinger Schmitt & Zúñiga-Pflücker116 Experimental murine models, strains Mouse: C57BL/6J mice Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000664 Mouse: Rag1− /− : B6.129S7-Rag1tm1Mom/J Jackson Laboratory RRID:IMSR_JAX:002096 Mouse: Rag2− /− Il2rg− /− Cao et al.117 Veronika Sexl Mouse: IL17A-IRES-GFP-KI reporter: C57BL/6-Il17atm1Bcgen/J Jackson Laboratory RRID: IMSR_JAX:018472 Mouse: Tec− /− Rag1− /− IL-17AeGFP: C57BL/6Il17atm1Bcgen/J x Tectm1Welm x B6.129S7-Rag1tm1Mom/J This study N/A Mouse: Dectin-1− /− : B6.129S6-Clec7atm1Gdb/J Taylor et al.118 RRID:IMSR_JAX:012337 Mouse: Dectin-2− /− : Clec4ntm1Yiw Saijo et al.119 MGI:4459637 Mouse: Tlr2/− : Tlr2tm1Aki Takeuchi et al.120 MGI:2178675 Mouse: Tlr4− /− : Tlr4tm1Aki Hashino et al.121 MGI:1860885 Mouse: Tec− /− : Tectm1Welm Ellmeier et al.34 MGI:2450883 Oligonucleotides m-Eef1a forward/reverse (5′-3′): ACGAGGCAATGTTG CTGGTGAC/GTGTGACAATCCAGAACAGGAGC Origene Cat#MP204369; GenBank:NM_010106 m-Tgfb1 forward/reverse (5′-3′): TGACGTCACTGGA GTTGTACGG/GGTTCATGTCATGGATGGTGC N/A GenBank:NM_011577.2 m-Il1b forward/reverse (5′-3′): (CCAACAAGTGATAT TCTCCATGAG/TCTTTCATTACACAGGACAGGT) N/A GenBank:NM_008361.4 (Continued on next page) Cell Reports 45, 117140, April 28, 2026 23

    Saline:

    Article Title: Optimization of Erythrocyte Lysis Protocols for Robust and Reproducible T Cell Analysis in Murine Peripheral Blood, Spleen, Lung, and Bone Marrow.
    Article Snippet: .. Antigen Clone Fluorochrome Dilution Surface/intracellular Fixable Viability Stain 620 — FVS620 1:1000 Surface Ghost Dye Violet 540 fixable viability dye — Violet 540 1:5000 Surface CD45 30-F11 PE-Cy7 3:1000 Surface CD3 17A2 BV510 1:200 Surface CD3 17A2 FITC 1:500 Surface CD4 RM4-5 APC 1:800 Surface CD4 GK1.5 PE/Dazzle 594 1:800 Surface CD8a 53-6.7 FITC 1:500 Surface CD8a 53-6.7 APC 1:800 Surface Ghost Dye Violet 540 fixable viability dye TONBO Cat#72086 Anti-CD45 antibody BD Cat#552848 Anti-CD3 antibody BioLegend Cat#100234 Anti-CD3 antibody BioLegend Cat#100204 Anti-CD4 antibody BD Cat#553051 Anti-CD4 antibody BioLegend Cat#100456 Anti-CD8a antibody BioLegend Cat#100706 Anti-CD8a antibody BioLegend Cat#100712 Lysing solution 10x concentrate BD Cat#349202 RBC lysis buffer (10x) BioLegend Cat#420301 Red blood cell lysis buffer Biosharp Cat#BL503B 3% acetic acid with methylene blue Stemcell Cat#07060 Fetal bovine serum (FBS) ExCell Cat#FSP500 Albumin from bovine serum Macklin Cat#B917420-200g Phosphate-buffer saline (PBS) Solarbio Cat#G0002 MACS tissue storage solution Miltenyi Cat#130-100-008 Lung dissociation kit, mouse Miltenyi Cat130-095-927 gentleMACS 25C Tubes C Miltenyi Cat#130-093-237 70 μm cell strainers Biosharp Cat#BS-70-XBS-N1 Heparin sodium anticoagulant tube 1.5mL Solarbio Cat#YA1471 Isoflurane anesthetic RWD Cat#R510-22-10 4 of 19 Journal of Immunology Research, 2026 1607, 2026, 1, D ow nloaded from https://onlinelibrary.w iley.com /doi/10.1155/jim r/3335332 by IN A SP - N E PA L , W iley O nline L ibrary on [10/04/2026]. ..

    Article Title: Innate lymphoid cells integrate sensing and plasticity to control fungal infections
    Article Snippet: Cat# 65-0840-90 Cyanine5 Streptavidin Biolegend Cat#405209 APC-Fire750 Streptavidin Biolegend Cat#405250 Streptavidin-DyLight 488 (currently marketed as Alexa Fluor 488) Jackson ImmunoResearch Cat#016-540-084 7-AAD Viability Staining Solution Biolegend Cat#420403 Apotracker Green Biolegend Cat#427401 Zombie Aqua Fixable Viability Kit Biolegend Cat#423102 Zombie NIR Fixable Viability Kit Biolegend Cat#423105 Zombie Violet Fixable Viability Kit Biolegend Cat#423113 Collagenase II Gibco; Fisher Scientific Cat# 17101015 DNAse I Sigma-Aldrich Cat#10104159001 Percoll GE-Healthcare Cat#GE17-0891-01 Recombinant Mouse IL-2 Biolegend Cat#575404 Recombinant Mouse IL-7 Biolegend Cat#577802 Recombinant Mouse SCF Miltenyi Cat#130-101-693 Recombinant Mouse IL-1β MedchemExpress Cat# MCE-HY-P7073A-2μg Recombinant Mouse IL-23 Biolegend Cat#589002 Recombinant Mouse IL-17C BioTechne Cat#2306-ML-025 Recombinant Rat/Mouse TGFβ1 MedchemExpress MCE-HY-P7117-2μg Brefeldin A Biolegend Cat#420601 Phorbol myristate acetate (PMA) Sigma-Aldrich Cat#P1585 Ionomycin Sigma-Aldrich Cat#IO634 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D2438 Zymosan Sigma-Aldrich Cat#Z4250 Curdlan Invivogen Cat#tlrl-cura Laminarin Invivogen Cat#tlrl-lam Chitin Wagener et al.115 N/A Dynasore hydrate Sigma-Aldrich Cat#D7693 R406 (Syk Inhibitor) Selleckchem Cat#S2194 α-D-Mannan Sigma-Aldrich Cat#M7504 Ketamin: Ketasol Livisto GTIN# 04050478000336 Xylazine: Sedaxylan Dechra GTIN# 08714225157464 Intracellular Staining Permeabilization Wash Buffer (10X) Biolegend Cat#421002 Fixation Buffer Biolegend Cat#420801 (Continued on next page) 22 Cell Reports 45, 117140, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Red Blood Cell Lysis Buffer (10X) Biolegend Cat#420302 True-Phos Perm Buffer Biolegend Cat#425401 Dulbecco’s Phosphate Buffered Saline Sigma-Aldrich Cat#8537 Hanks’ Balanced Salt solution Sigma-Aldrich Cat#8264 IMDM (Iscove’s Modified Dulbecco’s Medium) Lonza Cat#12-722F RPMI 1640 Medium Gibco; Fisher Scientific Cat#21875091 GlutaMAX Supplement Gibco; Fisher Scientific Cat#35050061 HEPES (1M) Gibco; Fisher Scientific Cat#15630080 Sodium pyruvate solution,100 mM Sigma-Aldrich Cat#S8636 MEM Non-essential Amino Acid Solution (100X) Sigma-Aldrich Cat#M7145 RNAlater Sigma-Aldrich Cat#R0901 z-IETD-FMK MedchemExpress Cat#MCE-HY-101297-1mg Necrostatin-1 MedchemExpress Cat#HY-15760 Ultra PureTM Distilled DNAse/RNAse free Water Invitrogen; Fisher Scientific Cat#10977049 Commercial assays Lineage cell depletion kit, mouse Miltenyi Cat130-090-858 Foxp3/Transcription Factor Staining Buffer Set-1 kit eBioscience, Fisher Scient. .. Cat#00-5523-00 System for Reverse Transcription Using AMV RT Promega Cat#A3500 SsoAdvanced Universal SYBR Green Supermix Biorad Cat#1725271 QIAGEN RNeasy Plus Micro Kit Quiagen Cat#74034 Monarch Spin RNA Cleanup Kit (10 μg) New England Biolabs Cat#T2030L Deposited data Mass Spectrometry of culture supernatants (ILC-Cgl interaction) ProteomeXchange Consortium111 PRIDE:PXD061271 Pulmonary ILC Sequencing (Smart-Seq2) GEO-database GEO:GSE293220 RNA-Sequencing of infected lung tissues after ILC-transfer GEO-database GEO:GSE293054 Experimental models cell lines Feeder cells: OP9-DL1 Gift of Meinrad Busslinger Schmitt & Zúñiga-Pflücker116 Experimental murine models, strains Mouse: C57BL/6J mice Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000664 Mouse: Rag1− /− : B6.129S7-Rag1tm1Mom/J Jackson Laboratory RRID:IMSR_JAX:002096 Mouse: Rag2− /− Il2rg− /− Cao et al.117 Veronika Sexl Mouse: IL17A-IRES-GFP-KI reporter: C57BL/6-Il17atm1Bcgen/J Jackson Laboratory RRID: IMSR_JAX:018472 Mouse: Tec− /− Rag1− /− IL-17AeGFP: C57BL/6Il17atm1Bcgen/J x Tectm1Welm x B6.129S7-Rag1tm1Mom/J This study N/A Mouse: Dectin-1− /− : B6.129S6-Clec7atm1Gdb/J Taylor et al.118 RRID:IMSR_JAX:012337 Mouse: Dectin-2− /− : Clec4ntm1Yiw Saijo et al.119 MGI:4459637 Mouse: Tlr2/− : Tlr2tm1Aki Takeuchi et al.120 MGI:2178675 Mouse: Tlr4− /− : Tlr4tm1Aki Hashino et al.121 MGI:1860885 Mouse: Tec− /− : Tectm1Welm Ellmeier et al.34 MGI:2450883 Oligonucleotides m-Eef1a forward/reverse (5′-3′): ACGAGGCAATGTTG CTGGTGAC/GTGTGACAATCCAGAACAGGAGC Origene Cat#MP204369; GenBank:NM_010106 m-Tgfb1 forward/reverse (5′-3′): TGACGTCACTGGA GTTGTACGG/GGTTCATGTCATGGATGGTGC N/A GenBank:NM_011577.2 m-Il1b forward/reverse (5′-3′): (CCAACAAGTGATAT TCTCCATGAG/TCTTTCATTACACAGGACAGGT) N/A GenBank:NM_008361.4 (Continued on next page) Cell Reports 45, 117140, April 28, 2026 23

    Magnetic Cell Separation:

    Article Title: Optimization of Erythrocyte Lysis Protocols for Robust and Reproducible T Cell Analysis in Murine Peripheral Blood, Spleen, Lung, and Bone Marrow.
    Article Snippet: .. Antigen Clone Fluorochrome Dilution Surface/intracellular Fixable Viability Stain 620 — FVS620 1:1000 Surface Ghost Dye Violet 540 fixable viability dye — Violet 540 1:5000 Surface CD45 30-F11 PE-Cy7 3:1000 Surface CD3 17A2 BV510 1:200 Surface CD3 17A2 FITC 1:500 Surface CD4 RM4-5 APC 1:800 Surface CD4 GK1.5 PE/Dazzle 594 1:800 Surface CD8a 53-6.7 FITC 1:500 Surface CD8a 53-6.7 APC 1:800 Surface Ghost Dye Violet 540 fixable viability dye TONBO Cat#72086 Anti-CD45 antibody BD Cat#552848 Anti-CD3 antibody BioLegend Cat#100234 Anti-CD3 antibody BioLegend Cat#100204 Anti-CD4 antibody BD Cat#553051 Anti-CD4 antibody BioLegend Cat#100456 Anti-CD8a antibody BioLegend Cat#100706 Anti-CD8a antibody BioLegend Cat#100712 Lysing solution 10x concentrate BD Cat#349202 RBC lysis buffer (10x) BioLegend Cat#420301 Red blood cell lysis buffer Biosharp Cat#BL503B 3% acetic acid with methylene blue Stemcell Cat#07060 Fetal bovine serum (FBS) ExCell Cat#FSP500 Albumin from bovine serum Macklin Cat#B917420-200g Phosphate-buffer saline (PBS) Solarbio Cat#G0002 MACS tissue storage solution Miltenyi Cat#130-100-008 Lung dissociation kit, mouse Miltenyi Cat130-095-927 gentleMACS 25C Tubes C Miltenyi Cat#130-093-237 70 μm cell strainers Biosharp Cat#BS-70-XBS-N1 Heparin sodium anticoagulant tube 1.5mL Solarbio Cat#YA1471 Isoflurane anesthetic RWD Cat#R510-22-10 4 of 19 Journal of Immunology Research, 2026 1607, 2026, 1, D ow nloaded from https://onlinelibrary.w iley.com /doi/10.1155/jim r/3335332 by IN A SP - N E PA L , W iley O nline L ibrary on [10/04/2026]. ..

    Binding Assay:

    Article Title: The transcription factor Helios restrains the anti-tumor capacity of CD8 + T cells.
    Article Snippet: Cas9 Nuclease V3 IDT Cat#1081058 Blasticidin S HCl Invitrogen Cat#R21001 ALV2 MedChemExpress Cat#HY-137206 BNTX maleate Abcam Cat#AB146142 KF 38789 Tocris Bioscience Cat#2748 SUN-B 8155 Tocris Bioscience Cat#2550 Adapalene Merck Cat#A7486 Ghost Dye Red 780 Tonbo Biosciences Cat#13-0865 Ghost Dye Red 710 Tonbo Biosciences Cat#13-0871 (Continued on next page) Cell Reports 44, 116680, December 23, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SYTOXTM Orange Dead Cell Stain Invitrogen Cat#S34861 Annexin V-APC Tonbo Biosciences Cat#20-6409 Annexin V Binding Buffer Tonbo Biosciences Cat#TNB-5000 Critical commercial assays Foxp3/Transcription Factor Stainning Buffer Kit Tonbo Biosciences Cat#TNB-0607 BD Cytofix/Cytoperm Plus BD Biosciences Cat#555028 TrueTagTM DNA Donor Kit Thermo Fisher Scientific Cat#A42992 Neon NxT Electroporation System Invitrogen Cat#NEON1S CD8a+ T cell Isolation Kit, mouse Miltenyi Cat130-104-075 ATAC-Seq Kit Active Motif Cat#53150 CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat#C34557 Deposited data scRNA-seq/ATAC-seq PRJEB101308 ENA (EMBL-EBI) Experimental models: Cell lines Jurkat E6.1 ATCC RRID:CVCL_0367 .. MC38 Gift from Dr. Santos Mañés, Centro Nacional de Biotecnologı́a/CSIC, Spain RRID:CVCL_B288 B16-F10 Gift from Dr. Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico RRID:CVCL_F936 B16-F10OVA Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A HTB-176 Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664; RRID:IMSR_JAX:000664 Mouse: C57BL/6-Tg(Cd8a-cre)1Itan/J The Jackson Laboratory Cat#008766; RRID:IMSR_JAX:008766 Mouse: B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ The Jackson Laboratory Cat#022071; RRID:IMSR_JAX:022071 Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory Cat#003831; RRID:IMSR_JAX:003831 Mouse: C57BL/6-Tg(CAG-OVAL)916Jen/J The Jackson Laboratory Cat#005145; RRID:IMSR_JAX:005145 Mouse: B6.129S7-Rag1tm1Mom/J The Jackson Laboratory Cat#002216; RRID:IMSR_JAX:002216 Mouse: PD-1− /− Gift from Dr. Arlene H. Sharpe (Harvard Medical School) N/A Mouse: Ikzf2-flox/flox Gift from Dr. Angela Thornton (NIAID) N/A Software and algorithms GraphPad Prism 10.1 GraphPad RRID: SCR_002798 http://www.graphpad.com/ NovoExpress Agilent RRID: SCR_024676 ImageJ NIH https://rsbweb.nih.gov/ij/ Cellpose 2.0 Ref. 64 RRID:SCR_021716; http://www.cellpose.org/ r-tidyverse R/Anaconda https://anaconda.org/conda-forge/r-tidyverse r-dplyr R/Anaconda https://anaconda.org/conda-forge/r-dplyr r-data.table R/Anaconda https://anaconda.org/conda-forge/r-data.table r-ggplot2 R/Anaconda https://anaconda.org/conda-forge/r-ggplot2 r-ggpubr R/Anaconda https://anaconda.org/conda-forge/r-ggpubr MiXCR Ref. 59 https://github.com/milaboratory/mixcr fastqc Anaconda https://anaconda.org/bioconda/fastqc trim-galore Anaconda https://anaconda.org/bioconda/trim-galore samtools Anaconda https://anaconda.org/bioconda/samtools (Continued on next page) 18 Cell Reports 44, 116680, December 23, 2025

    Electroporation:

    Article Title: The transcription factor Helios restrains the anti-tumor capacity of CD8 + T cells.
    Article Snippet: Cas9 Nuclease V3 IDT Cat#1081058 Blasticidin S HCl Invitrogen Cat#R21001 ALV2 MedChemExpress Cat#HY-137206 BNTX maleate Abcam Cat#AB146142 KF 38789 Tocris Bioscience Cat#2748 SUN-B 8155 Tocris Bioscience Cat#2550 Adapalene Merck Cat#A7486 Ghost Dye Red 780 Tonbo Biosciences Cat#13-0865 Ghost Dye Red 710 Tonbo Biosciences Cat#13-0871 (Continued on next page) Cell Reports 44, 116680, December 23, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SYTOXTM Orange Dead Cell Stain Invitrogen Cat#S34861 Annexin V-APC Tonbo Biosciences Cat#20-6409 Annexin V Binding Buffer Tonbo Biosciences Cat#TNB-5000 Critical commercial assays Foxp3/Transcription Factor Stainning Buffer Kit Tonbo Biosciences Cat#TNB-0607 BD Cytofix/Cytoperm Plus BD Biosciences Cat#555028 TrueTagTM DNA Donor Kit Thermo Fisher Scientific Cat#A42992 Neon NxT Electroporation System Invitrogen Cat#NEON1S CD8a+ T cell Isolation Kit, mouse Miltenyi Cat130-104-075 ATAC-Seq Kit Active Motif Cat#53150 CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat#C34557 Deposited data scRNA-seq/ATAC-seq PRJEB101308 ENA (EMBL-EBI) Experimental models: Cell lines Jurkat E6.1 ATCC RRID:CVCL_0367 .. MC38 Gift from Dr. Santos Mañés, Centro Nacional de Biotecnologı́a/CSIC, Spain RRID:CVCL_B288 B16-F10 Gift from Dr. Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico RRID:CVCL_F936 B16-F10OVA Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A HTB-176 Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664; RRID:IMSR_JAX:000664 Mouse: C57BL/6-Tg(Cd8a-cre)1Itan/J The Jackson Laboratory Cat#008766; RRID:IMSR_JAX:008766 Mouse: B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ The Jackson Laboratory Cat#022071; RRID:IMSR_JAX:022071 Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory Cat#003831; RRID:IMSR_JAX:003831 Mouse: C57BL/6-Tg(CAG-OVAL)916Jen/J The Jackson Laboratory Cat#005145; RRID:IMSR_JAX:005145 Mouse: B6.129S7-Rag1tm1Mom/J The Jackson Laboratory Cat#002216; RRID:IMSR_JAX:002216 Mouse: PD-1− /− Gift from Dr. Arlene H. Sharpe (Harvard Medical School) N/A Mouse: Ikzf2-flox/flox Gift from Dr. Angela Thornton (NIAID) N/A Software and algorithms GraphPad Prism 10.1 GraphPad RRID: SCR_002798 http://www.graphpad.com/ NovoExpress Agilent RRID: SCR_024676 ImageJ NIH https://rsbweb.nih.gov/ij/ Cellpose 2.0 Ref. 64 RRID:SCR_021716; http://www.cellpose.org/ r-tidyverse R/Anaconda https://anaconda.org/conda-forge/r-tidyverse r-dplyr R/Anaconda https://anaconda.org/conda-forge/r-dplyr r-data.table R/Anaconda https://anaconda.org/conda-forge/r-data.table r-ggplot2 R/Anaconda https://anaconda.org/conda-forge/r-ggplot2 r-ggpubr R/Anaconda https://anaconda.org/conda-forge/r-ggpubr MiXCR Ref. 59 https://github.com/milaboratory/mixcr fastqc Anaconda https://anaconda.org/bioconda/fastqc trim-galore Anaconda https://anaconda.org/bioconda/trim-galore samtools Anaconda https://anaconda.org/bioconda/samtools (Continued on next page) 18 Cell Reports 44, 116680, December 23, 2025

    Cell Isolation:

    Article Title: The transcription factor Helios restrains the anti-tumor capacity of CD8 + T cells.
    Article Snippet: Cas9 Nuclease V3 IDT Cat#1081058 Blasticidin S HCl Invitrogen Cat#R21001 ALV2 MedChemExpress Cat#HY-137206 BNTX maleate Abcam Cat#AB146142 KF 38789 Tocris Bioscience Cat#2748 SUN-B 8155 Tocris Bioscience Cat#2550 Adapalene Merck Cat#A7486 Ghost Dye Red 780 Tonbo Biosciences Cat#13-0865 Ghost Dye Red 710 Tonbo Biosciences Cat#13-0871 (Continued on next page) Cell Reports 44, 116680, December 23, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER SYTOXTM Orange Dead Cell Stain Invitrogen Cat#S34861 Annexin V-APC Tonbo Biosciences Cat#20-6409 Annexin V Binding Buffer Tonbo Biosciences Cat#TNB-5000 Critical commercial assays Foxp3/Transcription Factor Stainning Buffer Kit Tonbo Biosciences Cat#TNB-0607 BD Cytofix/Cytoperm Plus BD Biosciences Cat#555028 TrueTagTM DNA Donor Kit Thermo Fisher Scientific Cat#A42992 Neon NxT Electroporation System Invitrogen Cat#NEON1S CD8a+ T cell Isolation Kit, mouse Miltenyi Cat130-104-075 ATAC-Seq Kit Active Motif Cat#53150 CellTrace Violet Cell Proliferation Kit Thermo Fisher Scientific Cat#C34557 Deposited data scRNA-seq/ATAC-seq PRJEB101308 ENA (EMBL-EBI) Experimental models: Cell lines Jurkat E6.1 ATCC RRID:CVCL_0367 .. MC38 Gift from Dr. Santos Mañés, Centro Nacional de Biotecnologı́a/CSIC, Spain RRID:CVCL_B288 B16-F10 Gift from Dr. Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico RRID:CVCL_F936 B16-F10OVA Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A HTB-176 Gift from Laura Bonifaz, Instituto Mexicano del Seguro Social, Mexico N/A Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat#000664; RRID:IMSR_JAX:000664 Mouse: C57BL/6-Tg(Cd8a-cre)1Itan/J The Jackson Laboratory Cat#008766; RRID:IMSR_JAX:008766 Mouse: B6.Cg-Tg(Cd4-cre)1Cwi/BfluJ The Jackson Laboratory Cat#022071; RRID:IMSR_JAX:022071 Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J The Jackson Laboratory Cat#003831; RRID:IMSR_JAX:003831 Mouse: C57BL/6-Tg(CAG-OVAL)916Jen/J The Jackson Laboratory Cat#005145; RRID:IMSR_JAX:005145 Mouse: B6.129S7-Rag1tm1Mom/J The Jackson Laboratory Cat#002216; RRID:IMSR_JAX:002216 Mouse: PD-1− /− Gift from Dr. Arlene H. Sharpe (Harvard Medical School) N/A Mouse: Ikzf2-flox/flox Gift from Dr. Angela Thornton (NIAID) N/A Software and algorithms GraphPad Prism 10.1 GraphPad RRID: SCR_002798 http://www.graphpad.com/ NovoExpress Agilent RRID: SCR_024676 ImageJ NIH https://rsbweb.nih.gov/ij/ Cellpose 2.0 Ref. 64 RRID:SCR_021716; http://www.cellpose.org/ r-tidyverse R/Anaconda https://anaconda.org/conda-forge/r-tidyverse r-dplyr R/Anaconda https://anaconda.org/conda-forge/r-dplyr r-data.table R/Anaconda https://anaconda.org/conda-forge/r-data.table r-ggplot2 R/Anaconda https://anaconda.org/conda-forge/r-ggplot2 r-ggpubr R/Anaconda https://anaconda.org/conda-forge/r-ggpubr MiXCR Ref. 59 https://github.com/milaboratory/mixcr fastqc Anaconda https://anaconda.org/bioconda/fastqc trim-galore Anaconda https://anaconda.org/bioconda/trim-galore samtools Anaconda https://anaconda.org/bioconda/samtools (Continued on next page) 18 Cell Reports 44, 116680, December 23, 2025

    other:

    Article Title: An SPP1-SOCS1 pathway constrains interferon responses in tumor-associated macrophages and shapes an immunosuppressive tumor microenvironment.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Protein Transport Inhibitor BD Bioscience Cat#555029 BD HorizonTM Brilliant Stain Buffer BD Bioscience Cat#566349 Recombinant Mouse Osteopontin/OPN Protein R&D Cat#441-OP-050 Recombinant Osteopontin/OPN, Mouse (HEK293, His) MCE Cat#HY-P78358 Recombinant IFN-alpha 14, Mouse MCE Cat#HY-P76401 Recombinant IFN-beta, Mouse MCE Cat#HY-P73130 Recombinant IFN-gamma, Mouse MCE Cat#HY-P70667 Azoxymethane (AOM) MP Biomedicals Cat#2180139.1 Dextran Sodium Sulfate (DSS) MP Biomedical Cat#216011080 SIS3 SELLECK Cat#S7959 Stattic MCE Cat#HY-13818 Galunisertib MCE Cat#HY-13226 Ciforadenant MCE Cat#HY-101978 Corn Oil MCE Cat#HY-Y1888 DMSO SIGMA Cat#D8418 Recombinant Murine IL-2 PEPROTECH Cat#212-12 Recombinant Murine IL-4 PEPROTECH Cat#214-14 Recombinant Murine IL-10 PEPROTECH Cat#210-10 Recombinant Murine IL-12 p70 PEPROTECH Cat#210-12 Recombinant IL-13, Mouse MCE Cat#HY-P70460 Recombinant TGF beta 1/TGFB1, Mouse MCE Cat#HY-P7117 Bafilomycin A1 MCE Cat#HY-100558 Bortezomib MCE Cat#HY-10227 Recombinant Murine MCSF PEPROTECH Cat#315-02 D-Luciferin, Potassium Salt Goldbio Cat#LUCK-2G Critical commercial assays Zombie NIRTM Fixable Viability Kit Biolegend Cat#423106 Tumor Dissociation Kit, mouse MILTENYI Cat#130-096-730 EasySepTM Mouse CD4+ T Cell Isolation Kit STEMCELL Cat#19852 EasySepTM Mouse CD8+ T Cell Isolation Kit STEMCELL Cat#19853 RNeasy Mini Kit QIAGEN Cat# 74104 FOXP3/Transcription Factor Staining Buffer Set Thermo Fisher Cat# 00-5532-00 RNA isolater Total RNA Extraction Reagent Vazyme Cat# R401-01-AA PrimeScript RT Reagent Kit Takara Cat# RR047A TB Green Premix Ex Taq kit Takara Cat# RR420A Anti-Flag Nanobody IP kit (Magarose) AlpaLifeBio Cat# KTSM1361 mMESSAGE mMACHINETM T7 Transcription Kit Thermo Fisher Cat#AM1344 LipofectamineTM MessengerMAXTM Transfection Reagent Thermo Fisher Cat#LMRNA001 HiPerFect Transfection Reagent QIAGEN Cat#301704 QIAquick Gel Extraction Kit QIAGEN Cat#28704 Anti-Flag Nanobody IP kit (Magarose) AlpaLifeBio Cat#KTSM1361 PANO 7-plex IHC kit Panovue Cat#10217100100 Deposited data Processed Bulk RNA-seq data This paper https://doi.org/10.6084/m9.figshare.

    Article Title: Anchored screening identifies transcription factor blueprints underlying dendritic cell diversity and subset-specific anti-tumor immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant DNA pFUW-UbC-M2rtTA Rudolph Jaenisch, via Addgene RRID: Addgene_20342 psPAX2 Didier Trono, via Addgene RRID: Addgene_12260 pMD2.G Didier Trono, via Addgene RRID: Addgene_12259 pFUW-TetO-PU.1 Rosa et al.35 RRID: Addgene_139839 pFUW-TetO-AEBP2 This paper RRID: Addgene_207183 pFUW-TetO-ARID5B This paper RRID: Addgene_207184 pFUW-TetO-ASB2 This paper RRID: Addgene_207185 pFUW-TetO-BHLHE40 This paper RRID: Addgene_207186 pFUW-TetO-BCL6 Rosa et al.35 RRID: Addgene_139816 pFUW-TetO-E2F2 This paper RRID: Addgene_207187 pFUW-TetO-EGR2 This paper RRID: Addgene_207188 pFUW-TetO-HLX This paper RRID: Addgene_207189 pFUW-TetO-IRF2 Rosa et al.35 RRID: Addgene_139814 pFUW-TetO-IRF4 Rosa et al.35 RRID: Addgene_139804 pFUW-TetO-JUNB Rosa et al.36 RRID: Addgene_178441 pFUW-TetO-KCNIP3 This paper RRID: Addgene_207190 pFUW-TetO-KLF4 Rosa et al.35 RRID: Addgene_139828 pFUW-TetO-NFATC2 This paper RRID: Addgene_207191 pFUW-TetO-NFIX This paper RRID: Addgene_207192 pFUW-TetO-NFKB1 Rosa et al.35 RRID: Addgene_139822 pFUW-TetO-NOTCH2 This paper RRID: Addgene_207193 pFUW-TetO-NR4A1 This paper RRID: Addgene_207194 pFUW-TetO-POU2F2 This paper RRID: Addgene_207195 pFUW-TetO-PRDM1 This paper RRID: Addgene_207196 pFUW-TetO-RBPJ This paper RRID: Addgene_207197 pFUW-TetO-RELB Rosa et al.35 RRID: Addgene_139810 pFUW-TetO-RORC This paper RRID: Addgene_207198 pFUW-TetO-RUNX3 Rosa et al.35 RRID: Addgene_139812 pFUW-TetO-STAT3 Rosa et al.35 RRID: Addgene_139805 pFUW-TetO-STAT4 This paper RRID: Addgene_207199 pFUW-TetO-STAT5A Rosa et al.35 RRID: Addgene_139832 pFUW-TetO-TBX21 This paper RRID: Addgene_207233 pFUW-TetO-TCF7 This paper RRID: Addgene_207200 pFUW-TetO-TGIF1 This paper RRID: Addgene_207201 pFUW-TetO-TRPS1 This paper RRID: Addgene_207202 pFUW-TetO-ZBTB46 Rosa et al.35 RRID: Addgene_139811 pFUW-TetO-ZEB2 This paper RRID: Addgene_207203 pFUW-TetO-IRF8 Rosa et al.35 RRID: Addgene_139838 pFUW-TetO-ARID3A This paper RRID: Addgene_207204 pFUW-TetO-ARID5A This paper RRID: Addgene_207205 pFUW-TetO-BCL11A Rosa et al.35 RRID: Addgene_139809 pFUW-TetO-CBFA2T3 This paper RRID: Addgene_207206 pFUW-TetO-CREB3L2 This paper RRID: Addgene_207207 pFUW-TetO-ETS1 This paper RRID: Addgene_207208 pFUW-TetO-EYA1 This paper RRID: Addgene_207209 pFUW-TetO-FOXP1 This paper RRID: Addgene_207210 pFUW-TetO-HDAC5 This paper RRID: Addgene_207211 pFUW-TetO-HHEX This paper RRID: Addgene_207212 (Continued on next page) ll OPEN ACCESSArticle Immunity 58, 1–20.e1–e13, October 14, 2025 e5

    Single Cell:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Gene Expression:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Blocking Assay:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Amplification:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Polymer:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Labeling:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    RNA Sequencing:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Spatial Transcriptomics:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Sequencing:

    Article Title: Hypoxia shapes both therapeutic response and resistance in metastatic clear cell renal cell carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Human ccRCC tumor frozen or FFPE sections MSKCC Mouse KVpR tumors This paper N/A Mouse C57BL/6J syngeneic ccRCC tumors This paper N/A Healthy adult tonsil tissue Mount Sinai Hospital Surgical Pathology N/A Chemicals, peptides, and recombinant proteins Lenvatinib (E7080) Selleckchem/MedChemExpress Cat #S1164/HY-10981 BLZ945 (CSF1Ri; Soluletinib) Selleckchem/MedChemExpress Cat #S7725/HY-12768 Tamoxifen citrate chow, 400ppm Envigo N/A, discontinued Tamoxifen Sigma-Aldrich Cat #T5648 human recombinant M-CSF STEMCELL technologies Cat # 78057 Cobalt(II) chloride hexhydrate Sigma-Aldrich Cat #C8661 Hypoxyprobe HypoxyprobeTM N/A DAPI BD Pharmingen Cat # 564907 Calcein AM Invitrogen Cat #C3100MP Ack Lysing buffer Gibco Cat # A10492-01 Liberase TM Roche Cat # 5401119001 Collagenase Type II STEMCELL Technologies Cat # 07419 Percoll Cytiva Cat # 17-0891-01 Zombie NIR dye Biolegend Cat # 77184 TruStain FcX (anti-mouse CD16/32) Biolegend Cat # 101320 UltraComp eBeads compensation beads Invitrogen Cat # 01-2222-42 phorbol 12-myristate 13-acetate Sigma-Aldrich Cat #P8139 Ionomycin calcium salt Sigma-Aldrich Cat #I0634 Golgi-Stop BD Biosciences Cat # 51-2092KZ ImmunoCult SF macrophage medium STEMCELL technologies Cat # 10961 Sodium Carboxymethyl Cellulose Sigma-Aldrich Cat # 419273 Corn oil MedChem Express Cat # HY-Y1888 Tween 80 Sigma-Aldrich Cat #P8074 DNAase I Sigma-Aldrich Cat # DN25 Cryostor 10 Biolife Solutions Cat # 210102 Advanced DMEM/F-12 (Dulbecco’s Modified Eagle Medium/Ham’s F-12) Gibco Cat # 12634028 Prostaglandin E1 Sigma-Aldrich Cat #P7527 Triiodothyronine Sigma-Aldrich Cat #T5516 Hydrocortisone Sigma-Aldrich Cat #H0396 Epidermal growth factor Invitrogen Cat # 13247051 GlutaMAX Thermo Fisher Scientific Cat # 3505061 Penicillin-Streptomycin Thermo Scientific Cat # 15140122 Fetal Bovine Serum Fisherbrand Cat # FB12999102 Cytoseal XYL Thermo Scientific Cat # 8312-4 TRIzol reagent ThermoFisher Cat # 15596018 Bovine Serum Albumin Sigma-Aldrich Cat # A3059-50G Horse Serum Sigma-Aldrich Cat #H0146-5ML Cell-ID Intercalator: Iridium 500 uM Standard Biotools Cat # 201192B Antibody Stabilizer, PBS base Candor Biosciences Cat # 131-125(BC) Critical commercial assays EasySep human monocyte enrichment kit without CD16 depletion STEMCELL technologies Cat # 19058 Human Osteopontin Quantikine ELISA kit R&D systems Cat #D0ST00 (Continued on next page) ll OPEN ACCESSArticle Cancer Cell 44, 1–19.e1–e15, July 13, 2026 e4 .. REAGENT or RESOURCE SOURCE IDENTIFIER Tumor Dissociation Kit, human Miltenyi Cat # 130-095-929 Tumor Dissociation Kit, mouse Miltenyi Cat # 130-096-730 Chromium Next GEM Single Cell 5′ mRNA V2 Kit 10X Genomics PN-1000263 Library Construction Kit 10X Genomics PN-1000190 Chromium Next GEM Chip K Single Cell Kit 10X Genomics PN-1000287 Dual Index Kit TT Set A 10X Genomics PN-1000215 Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome 10X Genomics PN-1000336 miRNeasy Micro kit Qiagen Cat # 217084 miRNeasy Mini kit Qiagen Cat # 217004 RNeasy FFPE Kit Qiagen Cat # 73504 MagMAX FFPE DNA/RNA Ultra Kit Thermofisher Cat # A31881 Foxp3/Transcription Factor Staining Buffer Kit Cytek Biosciences Cat # TNB-06070KIT TruSeq Stranded Total RNA LT Kit Illumina Cat # RS-122-1202 AllPrep DNA/RNA FFPE Kit Qiagen Cat # 80234 Citrate-Based Antigen Unmasking Solution Vector Laboratories Cat # H-3300-250 BLOXALL Blocking Solution Vector Laboratories Cat # SP-6000-100 ImmPRESS Excel Amplified anti-Rabbit IgG HRP Polymer Staining Kit Vector Laboratories Cat # MP-7601-50 VECTASTAIN Elite ABC-HRP Kit Vector Laboratories Cat # PK-6101 MaxparTM X8 Multi-Metal Labeling Kit40 Rxn Standard Biotools Cat # 201300 Deposited data Raw mouse scRNA-seq data This paper GEO: GSE293450 Raw and processed human MSKCC RWD bulk RNA-seq data This paper GEO: GSE293952 Raw human scRNA-seq data This paper GEO: GSE294109 Raw human Visium spatial transcriptomics data This paper GEO: GSE294006 Experimental models: Cell lines LVRCC67 Rappold, Vuong et al.43 2022 N/A LVRCC67-LM2 This paper N/A LVRCC88 This paper N/A LVRCC88-M1 This paper N/A Experimental models: Organisms/strains Mouse: KspCreERT2;Vhlf/f;Trp53f/f;Rb1f/f (KVpR) Harlander et al.28 2017 N/A Mouse: C57BL/6J Jackson Laboratories Strain # 000664 Oligonucleotides Vhl sgRNA targeting sequence: CCCGGTGGTAAGATCGGGTA This paper N/A Trp53 sgRNA targeting sequence: ACCCTGTCACCGAGACCCC This paper N/A Rb1 sgRNA targeting sequence: TGCGCGGGGTCGTCCTCCCG This paper N/A Primer: Vhl sgRNA cut site forward: GACCCGTTCCAATAATGCCC This paper N/A Primer: Vhl sgRNA cut site reverse: GCAAACCTCTAAGCTCGGTG This paper N/A (Continued on next page) ll OPEN ACCESS Article e5 Cancer Cell 44, 1–19.e1–e15, July 13, 2026 ..

    Modification:

    Article Title: Innate lymphoid cells integrate sensing and plasticity to control fungal infections
    Article Snippet: Cat# 65-0840-90 Cyanine5 Streptavidin Biolegend Cat#405209 APC-Fire750 Streptavidin Biolegend Cat#405250 Streptavidin-DyLight 488 (currently marketed as Alexa Fluor 488) Jackson ImmunoResearch Cat#016-540-084 7-AAD Viability Staining Solution Biolegend Cat#420403 Apotracker Green Biolegend Cat#427401 Zombie Aqua Fixable Viability Kit Biolegend Cat#423102 Zombie NIR Fixable Viability Kit Biolegend Cat#423105 Zombie Violet Fixable Viability Kit Biolegend Cat#423113 Collagenase II Gibco; Fisher Scientific Cat# 17101015 DNAse I Sigma-Aldrich Cat#10104159001 Percoll GE-Healthcare Cat#GE17-0891-01 Recombinant Mouse IL-2 Biolegend Cat#575404 Recombinant Mouse IL-7 Biolegend Cat#577802 Recombinant Mouse SCF Miltenyi Cat#130-101-693 Recombinant Mouse IL-1β MedchemExpress Cat# MCE-HY-P7073A-2μg Recombinant Mouse IL-23 Biolegend Cat#589002 Recombinant Mouse IL-17C BioTechne Cat#2306-ML-025 Recombinant Rat/Mouse TGFβ1 MedchemExpress MCE-HY-P7117-2μg Brefeldin A Biolegend Cat#420601 Phorbol myristate acetate (PMA) Sigma-Aldrich Cat#P1585 Ionomycin Sigma-Aldrich Cat#IO634 Dimethyl sulfoxide (DMSO) Sigma-Aldrich Cat#D2438 Zymosan Sigma-Aldrich Cat#Z4250 Curdlan Invivogen Cat#tlrl-cura Laminarin Invivogen Cat#tlrl-lam Chitin Wagener et al.115 N/A Dynasore hydrate Sigma-Aldrich Cat#D7693 R406 (Syk Inhibitor) Selleckchem Cat#S2194 α-D-Mannan Sigma-Aldrich Cat#M7504 Ketamin: Ketasol Livisto GTIN# 04050478000336 Xylazine: Sedaxylan Dechra GTIN# 08714225157464 Intracellular Staining Permeabilization Wash Buffer (10X) Biolegend Cat#421002 Fixation Buffer Biolegend Cat#420801 (Continued on next page) 22 Cell Reports 45, 117140, April 28, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Red Blood Cell Lysis Buffer (10X) Biolegend Cat#420302 True-Phos Perm Buffer Biolegend Cat#425401 Dulbecco’s Phosphate Buffered Saline Sigma-Aldrich Cat#8537 Hanks’ Balanced Salt solution Sigma-Aldrich Cat#8264 IMDM (Iscove’s Modified Dulbecco’s Medium) Lonza Cat#12-722F RPMI 1640 Medium Gibco; Fisher Scientific Cat#21875091 GlutaMAX Supplement Gibco; Fisher Scientific Cat#35050061 HEPES (1M) Gibco; Fisher Scientific Cat#15630080 Sodium pyruvate solution,100 mM Sigma-Aldrich Cat#S8636 MEM Non-essential Amino Acid Solution (100X) Sigma-Aldrich Cat#M7145 RNAlater Sigma-Aldrich Cat#R0901 z-IETD-FMK MedchemExpress Cat#MCE-HY-101297-1mg Necrostatin-1 MedchemExpress Cat#HY-15760 Ultra PureTM Distilled DNAse/RNAse free Water Invitrogen; Fisher Scientific Cat#10977049 Commercial assays Lineage cell depletion kit, mouse Miltenyi Cat130-090-858 Foxp3/Transcription Factor Staining Buffer Set-1 kit eBioscience, Fisher Scient. .. Cat#00-5523-00 System for Reverse Transcription Using AMV RT Promega Cat#A3500 SsoAdvanced Universal SYBR Green Supermix Biorad Cat#1725271 QIAGEN RNeasy Plus Micro Kit Quiagen Cat#74034 Monarch Spin RNA Cleanup Kit (10 μg) New England Biolabs Cat#T2030L Deposited data Mass Spectrometry of culture supernatants (ILC-Cgl interaction) ProteomeXchange Consortium111 PRIDE:PXD061271 Pulmonary ILC Sequencing (Smart-Seq2) GEO-database GEO:GSE293220 RNA-Sequencing of infected lung tissues after ILC-transfer GEO-database GEO:GSE293054 Experimental models cell lines Feeder cells: OP9-DL1 Gift of Meinrad Busslinger Schmitt & Zúñiga-Pflücker116 Experimental murine models, strains Mouse: C57BL/6J mice Jackson Laboratory Cat#000664; RRID: IMSR_JAX:000664 Mouse: Rag1− /− : B6.129S7-Rag1tm1Mom/J Jackson Laboratory RRID:IMSR_JAX:002096 Mouse: Rag2− /− Il2rg− /− Cao et al.117 Veronika Sexl Mouse: IL17A-IRES-GFP-KI reporter: C57BL/6-Il17atm1Bcgen/J Jackson Laboratory RRID: IMSR_JAX:018472 Mouse: Tec− /− Rag1− /− IL-17AeGFP: C57BL/6Il17atm1Bcgen/J x Tectm1Welm x B6.129S7-Rag1tm1Mom/J This study N/A Mouse: Dectin-1− /− : B6.129S6-Clec7atm1Gdb/J Taylor et al.118 RRID:IMSR_JAX:012337 Mouse: Dectin-2− /− : Clec4ntm1Yiw Saijo et al.119 MGI:4459637 Mouse: Tlr2/− : Tlr2tm1Aki Takeuchi et al.120 MGI:2178675 Mouse: Tlr4− /− : Tlr4tm1Aki Hashino et al.121 MGI:1860885 Mouse: Tec− /− : Tectm1Welm Ellmeier et al.34 MGI:2450883 Oligonucleotides m-Eef1a forward/reverse (5′-3′): ACGAGGCAATGTTG CTGGTGAC/GTGTGACAATCCAGAACAGGAGC Origene Cat#MP204369; GenBank:NM_010106 m-Tgfb1 forward/reverse (5′-3′): TGACGTCACTGGA GTTGTACGG/GGTTCATGTCATGGATGGTGC N/A GenBank:NM_011577.2 m-Il1b forward/reverse (5′-3′): (CCAACAAGTGATAT TCTCCATGAG/TCTTTCATTACACAGGACAGGT) N/A GenBank:NM_008361.4 (Continued on next page) Cell Reports 45, 117140, April 28, 2026 23



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