Recombinant:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Molecular Weight:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Staining:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Immunoprecipitation:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Multiplex Assay:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Transfection:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
Luciferase:Article Title: A hierarchical Rorc(γt) cis-regulatory cascade orchestrates differentiation of RORγt⁺ innate immune cells.
Article Snippet: Medium, powder Thermo Fisher Scientific Cat#: 22600050 Collagenase D SIGMA Cat#11088882001 DNaseI SIGMA Cat#25D-10G; CAS# 9003-98-9 PercollTM system Cyvita 17089109 Fetal bovine serum (FBS) Cyvita SH30910.03 Alt-R® Recombinant Cas9 V3 iDT Cat# 1081060 Alt-R® CRISPR-Cas9 tracrRNA iDT Cat# 1072534 DAPI DOJINDO Cat# D523 Fixable Viability Dye eFluor 780 Thermo Fisher Scientific Cat# 65-0865-14 Fixable Viability Dye eFluor 506 Thermo Fisher Scientific Cat# 65-0866-14 BV605 Streptavidin BioLegend Cat# 405229 BV650 Streptavidin BioLegend Cat# 405232 Fluoromount-G solution. .. SouthernBiotech Cat# 0100-35 G-mount GenoStaff Cat# GM-01 Recombinant Mouse IL-23 R&D System Cat# 1887-ML-010/CF Recombinant Mouse IL-15 Pepro Tech Cat# 210-15-10 Recombinant Mouse IL-2 R&D System Cat# 402-ML-020/CF Recombinant Mouse IL-7 R&D System Cat# 407-ML-005/CF Recombinant Mouse IL-7 Pepro Tech Cat# 217-17-10UG Recombinant Mouse SCF Pepro Tech Cat# 250-03-10UG Brefeldin A Solution Thermo Fisher Scientific Cat# 00-4506-51 4-Ethoxymethylene-2-phenyl-2-oxazolin5-one (Oxazolone) SIGMA Cat# 862207-1G-A; CAS:15646-46-5 Dextran Sulfate Sodium (DSS) salt molecular weight, 36.000–50.000 MP Biomedicals Cat# MFCD00081551; CAS:9011-18-1 Isoflurane RIKEN IsofluraneRIKEN; CAS: 26675-46-7 All-trans retinoic acid Sigma-Aldrich Cat# R2625; CAS: 302-79-4 Formaldehyde Solution Nacalai Tesque Cat# 16223-55; CAS: 50-00-0 Acetate SIGMA Cat# 179124; CAS: 67-64-1 Corn oil SIGMA Cat# 47112; CAS: 47112 Critical commercial assays Foxp3/Transcriptional Factor Staining Buffer Set Thermo Fisher Scientific Cat#00-5523-00 ATAC-Seq Kit Active Motif Cat#53150 Chromatin Immunoprecipitation(ChIP) Assay Kit Sigma-Aldrich Cat#17-295 NEBNext Multiplex Oligos for Illumina (96 Unique Dual Index Primer Pairs) NEW ENGLAND Biolabs Cat#E6440 FuGENE® 6 Transfection Reagent Promega Cat# E2691 Dual-Glo® Luciferase Assay System Promega Cat# E2920 SMART-Seq® HT PLUS Kit Takara Bio Cat#R400749 SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio Cat#634889 AMPure XP beads Beckman Coulter Cat#A63880 (Continued on next page) e3 Immunity 59, 953–969.e1–e10, April 14, 2026 .. REAGENT or RESOURCE SOURCE IDENTIFIER Chromium Next GEM single cell 3’ library & Gel beads kit v3.1 10x Genomics Cat#1000128 Chromium Next GEM single cell G chip kit 10x Genomics Cat#1000127 Chromium i7 multiplex kit 10x Genomics Cat#120262 High Sensitivity DNA kit Agilent Cat#5067-4626 Qubit 1X dsDNA HS Assay Kit Thermo Fisher Scientific Cat#Q33230 Deposited data ATAC-seq Kearly et al.59; Weizman et al.54; Ito et al.55; Gao et al.56; and Habash et al.60 GSM8430804; GSM2785745; GSE270373; GSM7036250; GSM8493112 ChIP-seq Liu et al.62 and Wang et al.64 GSM7656352 and GSM4979627 CUT&Tag Itokawa et al.61 GSM5723333 CUT&RUN Mahajan et al.63 GSM4551384 ATAC-seq for fetal liver cells, ILC3s This study GSE278157 Single-cell RNA-seq This study GSE278161 Bulk RNA-seq_ChILP This study GSE278516 Bulk RNA-seq_vitro This study GSE278518 ChIP-seq (CBFβ) for E12.5 fetal liver cells This study GSE311597 ChIL-seq (CBFβ) for MNK3 cells This study GSE311596 ATAC-seq for Vav1Cre Cbfbflox/flox This study GSE311595 ATAC-seq for CNS11 mutants This study GSE311595 Experimental models: Cell lines Tst-4-DLL1 stroma cell Watanabe et al.74 N/A MNK-3 Mouse Innate Lymphoid Cell Line Sigma-Aldrich SCC628 HEK293T cells Abcam ab255449 Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Japan Strain#000664 Mouse: C57BL/6J SJL-PtprcaPepcb/BoyJ The Jackson Laboratory Strain#002014 Mouse: BDF1 (C57BL/6N x DBA/2) Japan SLC N/A Mouse: Runx3tdTomato Kojo et al.32 N/A Mouse: Cbfbflox Naoe et al.52 N/A Mouse: Il7r(Cd127)Cre Schlenner et al.51 N/A Mouse: Rorc(γt)Gfp Lochner et al.15 N/A Mouse: Vav1Cre Ogilvy et al.75 Jackson Laboraory Strain#000664 Mouse: Rag1-/- Mombaerts et al.76 Jackson Laboraory Strain#002216 Mouse: Rorc-/- This study N/A Mouse: Rorc CNS9Δ This study N/A Mouse: Rorc CNS9Runx This study N/A Mouse: Rorc CNS9RAR This study N/A Mouse: Rorc CNS11mut This study N/A Mouse: Rorc CNS114th This study N/A Mouse: Rorc CNS113wt This study N/A Mouse: LtaGFP This study N/A Oligonucleotides crRNA-1 for Rorc-/-; 5′- ACUUCUCAUGACUGAGAACU-3′ This study (iDT) N/A crRNA-2 for Rorc-/-; 5′- AGUCAUGAGAAGUAAGUGAA-3′ This study (iDT) N/A crRNA for LTaEGFP; 5′- CUUUAGAAUCUACAGUGCAA-3′ This study (iDT) N/A (Continued on next page) Immunity 59, 953–969.e1–e10, April 14, 2026 e4
|
R&D Systems is a verified supplier 
R&D Systems manufactures this product 