Staining:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
Membrane:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
SDS Page:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
SYBR Green Assay:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
DNA Extraction:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
Extraction:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
Reverse Transcription:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
Activity Assay:Article Title: Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-ADP-ribose (E6F6A) Cell Signaling Technologies Cat. # 83732S; RRID: AB_2749858 Anti-ethenoadenosine (1G4) Thermo Fisher Cat. # Ma1-40268; RRID: AB_1074293 Anti-vinculin (7F9) Sigma Cat. # 90227; RRID:AB_2304338 IRDye 680RD Goat anti-rabbit IgG LICOR Cat. # 926-68071; RRID: AB_10956166 IRDye 680RD Goat anti-mouse IgG LICOR Cat. # 926-68070; RRID: AB_2651128 Goat anti-rabbit alexa fluor 488 Thermo Fisher Cat. # A-11008; RRID: AB_143165 Donkey anti-mouse alexa fluor 488 Thermo Fisher Cat. # A-21202; RRID: AB_141607 Anti-paxillin (PXC-10) Thermo Fisher Cat. # MA1-24952; RRID: AB_795141 Anti-non-muscle myosin IIA antibody Abcam Cat. # ab75590; RRID: AB_10674199 Bacterial strains E. coli BL21 This study N/A E. coli DE3 This study N/A B. stercoris ATCC 43183 Koropatkin et al., 2008 N/A B. stercoris ATCC 43183 Dbxa This study N/A B. stercoris ATCC 43183 Dtdk This study N/A Biological samples Strains from human stool from non-IBD and IBD subjects PRISM cohort at MGH IRB ref # 2004-P-001067 Cell lines HT-29 cells ATCC Cat. # HTB-38 Caco-2 cells ATCC Cat. # HTB-37 U2OS cells ATCC Cat. # HTB-96 Chemicals and reagents Ethanol Sigma Cat. # 459836 Methanol Sigma Cat. # 34860 Inosine Sigma Cat. # I4125-10G Hemin Sigma Cat. # H9039-1G Vitamin K1 Sigma Cat. # V3501-5G M9 salts Teknova Cat. # M8008 Ampicillin Sigma Cat. # A0166 Gentamicin Sigma Cat. # G1397 Erythromycin Sigma Cat. # E0774 Kanamycin Sigma Cat. # 60615-5G Cellobiose Becton Dickinson Cat. # 216010 Maltose Hardy Diagnostics Cat. # C6220 Fructose Sigma Cat. # F0127 Glucose Sigma Cat. # 0188-1Kg (Continued on next page) e1 Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRITC-conjugated Phalloidin Sigma Cat. # 90228 DAPI Sigma Cat. # 90229 Hoechst Thermo Fisher Cat. #62249 SiR actin stain Cytoskeleton Cat. # CY-SC001 Fetal Bovine Serum Thermo Fisher Cat. # 10438026 Clickable NAD Biolog Cat. # N 055 NAD Sigma Cat. # 10128965001 Nicotinamide 1,N6-ethenoadenine dinucleotide (etheno-NAD) Sigma Cat. # N2630-5MG Fluorescein-NAD Trevigen Cat. # 4673-500-01 Tris-HCl pH 8.0 Thermo Fisher Cat. # 15568025 Imidazole Sigma Cat. # I2399-100G Arginine Sigma Cat. # A5006-100G DTT Sigma Cat. # 10197777001 PMSF Thermo Fisher Cat. # 36978 cOmplete mini-protease inhibitor cocktail (tabs) Sigma Cat. # 11836153001 EDTA Thermo Fisher Cat. # 15-575-020 Sodium chloride Sigma Cat. # S9888 Sucrose Sigma Cat. # S0389 Glycerol Thermo Fisher Cat. # 15514011 Nitrocellulose membrane Thermo Fisher Cat. # IB301002 PVDF membrane Thermo Fisher Cat. # IB401031 15-well 4-20% SDS-PAGE gels Bio-Rad Cat. # 4561095 SYBR green Thermo Fisher Cat. # A25742 Instant Blue gel stain Abcam Cat. # ab119211 His-Pur Nickel beads Thermo Fisher Cat. # 88221 Protein G Dynabeads Thermo Fisher Cat. # 1004D Tween 20 Sigma Cat. # P9416 Triton-X Sigma Cat. # X100 Paraformaldehyde Thermo Fisher Cat. # 28906 PBS VWR Cat. # 45000-446 Blebbistatin Sigma Cat. # B0560-1MG ML-9 Sigma Cat. # C1172-5MG Crystal Violet BD Biosciences Cat. # 212525 Commercial assay kits Qiagen RNeasy Plus Mini Kit Qiagen Cat. # 74136 Qiagen DNA extraction stool kit Qiagen Cat. # 51504 Qiagen Tissue extraction kit Qiagen Cat. # 69504 Legendplex Mouse Inflammation Kit Biolegend Cat. # 552364 SuperScript III reverse transcriptase kit Invitrogen Cat. # 18080051 Direct-Zol RNA MiniPrep Plus Zymo Research Cat. # R2060 Fluorometric Inosine Detection Kit Abcam Cat. # ab126286 ATP detection kit Abcam Cat. # ab113849 ADA activity assay kit Abcam Cat. # ab204695 Focal adhesion staining kit Sigma Cat. # FAK100 HiFi DNA Assembly Master Mix New England Biolabs Cat. # E2621S Q5 High Fidelity DNA Polymerase New England Biolabs Cat. # M0491S (Continued on next page) Cell Host & Microbe 29, 1351–1365.e1–e11, September 8, 2021 e2 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited Data Metabolomic analysis This study www.metabolomicsworkbench.org Project ID PR001176 RNA-sequencing data This study Sequence Read Archive (SRA), Project ID PRJNA742399 Experimental models C57BL/6N mice (Gnotobiotic) Taconic B6-M/F C57BL/6N mice (ASF) Taconic B6-M/F Plasmids pET28b-bxa-snap This study N/A pET28b-bxa-818-dbl-cat This study N/A pET28b-bxa-719-cat This study N/A pET28b-bxa-820-cat This study N/A pET28b-bxa This study N/A pKNOCK-bla-ermGb Laurie Comstock; Alexeyev, 1999 N/A pKNOCK_erm_BACSTE_02189 This study N/A pKNOCK_erm_tdk This study N/A Oligonucleotides (5’-3’)
|
Cytoskeleton Inc is a verified supplier 
Cytoskeleton Inc manufactures this product 