Chromatin Immunoprecipitation:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
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REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
Recombinant:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
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REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
Gene Expression:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
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REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
Reverse Transcription:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
Magnetic Cell Separation:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
Protease Inhibitor:Article Title: Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER APC-Cy7 anti-mouse Ter-119 antibody Biolegend RRID:AB_2137788 BUF373 anti-mouse ST2 antibody BD Biosciences RRID: AB_2873697 BV711 anti-human CD25 antibody Biolegend RRID:AB_2562910 APC anti-human CD4 antibody Biolegend RRID:AB_571945 BUV737 anti-human CD45 antibody BD Biosciences RRID:AB_2873123 PE anti-human CD45 antibody Miltenyi Biotec RRID:AB_2658239 BUV737 Streptavidin BD Biosciences RRID:AB_2869560 Goat Anti-Rabbit IgG (H+L) antibody, AF 647 Thermo Fisher Scientific RRID:AB_10562581 Goat Anti-Rabbit IgG (H+L) antibody, AF 594 Thermo Fisher Scientific RRID:AB_2940825 PE Rat IgG1, kappa isotype ctrl Biolegend RRID:AB_326513 eF660 Mouse IgG2b kappa isotype ctrl Thermo Fisher Scientific RRID:AB_11217883 Histone H3 (acetyl K27) antibody - ChIP Grade RRID:AB_2118291 Chemicals, Peptides, and Recombinant Proteins Recombinant human IL-2 Novartis Proleukin S 18 Mio U Recombinant human Tgf-b1 Peprotech Cat# 100-21 Recombinant murine IL-4 Peprotech Cat# 214-14 Recombinant murine IL-1b Peprotech Cat# 211-11B Recombinant murine IL-23 Biolegend Cat# 589002 InVivoMAb anti-mouse IFNg BioXCell Cat# BE0055 InVivoMAb anti-mouse IL-4 BioXCell Cat# BE0045 HBSS Gibco Cat# 14025092 PBS Gibco Cat# 10010023 DMEM Gibco Cat# 41965 Collagenase Type II Sigma-Aldrich Cat# C6885 Collagenase Type IV Sigma-Aldrich Cat# C5138 DNAse I Roche Cat# 11284932001 Bovine Serum Albumin Sigma Cat# A4503 Pancoll Pan Biotech Cat# #P04-601000 Taqman Gene Expression Master Mix Thermo Fisher Scientific Cat# 4359016 SuperScript II Reverse Transcriptase Thermo Fisher Scientific Cat# 18064071 Oligo d(T) 12-18 Primer Thermo Fisher Scientific Cat# 18418012 Compensation Beads eBiosciences Cat# 01-1111-41 Hair removal creme Reckitt Benckiser (Veet) N/A Fixable Viability Dye eFluor 780 eBioscience Cat# 65-0865-18 DAPI (4’,6-Diamidino-2-phenylindol) Sigma-Aldrich Cat#10236276001 Digitonin Thermo Fisher Scientific Cat# BN2006 Trizma Hydrochloride Solution, pH 7.4 Sigma Cat# T2194 Sodium Chloride Solution, 5 M Sigma Cat# 59222C Magnesium Chloride Solution, 1M Sigma Cat# M1028 Nonidet P40 Substitute Sigma Cat# 74385 MACS BSA Stock Solution Miltenyi Biotec Cat# 130-091-376 TWEEN 20 Sigma Cat# P9416 Phenylmethanesulfonyl fluoride (PMSF) Sigma-Aldrich 10837091001 Sodium butyrate (NaBut) Sigma-Aldrich 303410 cOmplete , EDTA-free Protease Inhibitor Cocktail Sigma-Aldrich 04693132001 Nonidet P40 Substitute (10%Sol) Sigma-Aldrich 11332473001 1 M Tris pH 7.4 Sigma-Aldrich T2194 (Continued on next page) Immunity 57, 1975–1993.e1–e10, August 13, 2024 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER 0.5 M EDTA pH 8.0 Merck Millipore 324506 20 % SDS Sigma-Aldrich 05030 2M KCl Sigma-Aldrich 60142 2M KOH Carl Roth 6751.3 Hepes 1M Hepes pH 7.9 Sigma-Aldrich H4034 Sodium deoxycholate Sigma-Aldrich D 6750 Proteinase K, recombinant, PCR Grade 20mg/ml Sigma-Aldrich 03115879001 (RPROTK-RO) 2.5 M LiCl Sigma-Aldrich L9650 PBS without CaCl2, MgCl2 Thermo Fisher Scientific 14190-094 1 M MgCl2 Sigma-Aldrich M1028 5 M NaCl Sigma-Aldrich 59222C 10 % Tween 20 Sigma-Aldrich P9416 10 % Triton x-100 Sigma-Aldrich T8787 NaHCO3 Sigma-Aldrich S5761 nProteinA Sepharose bead GE Healthcare 17-5280-04 nProteinG Sepharose beads GE Healthcare 17-0618-01 Sepharose CL-4B beads Sigma-Aldrich CL4B200-100ml Critical Commercial Assays GentleMACS C tube Miltenyi Biotec Cat# 130-096-334 Lamina Propria Dissociation Kit Miltenyi Biotec Cat# 130-097-410 CD45 Microbeads, mouse Miltenyi Biotec Cat# 130-052-301 LS column Miltenyi Biotec Cat# 130-042-401 ACK lysis buffer Gibco Cat# A1049201 Foxp3 / Transcription Factor Buffer Set eBiosciences Cat# 00-5523-00 RNEasy Plus Mini Kit Qiagen Cat# 74134 Immuprep Analytik Jena Analytik Jena Cat# 845-KS-2040250 Mouse T-cell activation and expansion kit Miltenyi Biotec Cat# 130-093-627 Foxp3 / Transcription Factor Staining Buffer Set eBioscience Cat# 00-5523-00 NEBNext Multiplex Oligos NEB Cat# E7335L Illumina DNA/RNA UD Indexes Illumina Cat #20091658 Chromium Single Cell Controller & Accessory Kit 10X Cat# 120212 Agencourt AMPure XP beads Beckman Coulter Cat# A63880 Qubit dsDNA HS Kit Thermo Fisher Scientific Cat# Q32851 High Sensitivity D1000 ScreenTape Agilent Cat# 50675584 High Sensitivity D1000 Reagents Agilent Cat# 50675585 Monarch PCR & DNA Cleanup Kit (5 mg) NEB Cat# T1030L NEBNext Ultra II DNA Library Prep Kit for Illumina NEB Cat #E7645L Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit v1.1 10X Cat# 1000175 Chromium Next GEM Chip H Single Cell Kit v1.1 10X Cat# 1000161 Chromium i7 Multiplex Kit N 10X Cat# 1000084 Deposited Data Raw and analyzed data: murine scATAC-seq, bulk ATAC-seq, and ChIP-seq, human scATAC-seq This manuscript GEO: GSE242466 (mouse data) EGA: EGAD50000000510 (human data) Experimental Models: Organisms/Strains Wildtype C57BL/6 Jackson Laboratories or Charles River Breeding Laboratories Strain #:000664 129S-Batftm1.1Kmm/J Jackson Laboratories Strain# 013757 Areg(GFP) BAC-transgenic mice Published in Delacher et al.22 N/A Foxp3tm1(CD2/CD52)Shori Published in Komatsu et al.58 N/A (Continued on next page) e3 Immunity 57, 1975–1993.e1–e10, August 13, 2024
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