Virus:Article Title: Dimethyl itaconate induces long-term innate immune responses and confers protection against infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BV785 anti-human CD11b antibody (ICRF44) Biolegend Cat#301346; RRID AB_2563794 Anti-H3K4me3 (polyclonal) Diagenode Cat#C15410003; RRID:AB_2924768 Anti-H3K9me3 (polyclonal) Diagenode Cat#C15410193; RRID:AB_2616044 Bacterial and virus strains Candida albicans (UC820 strain) ATCC ATCC MYA-3573 Staphylococcus aureus (RN4220 strain) 18 N/A Chemicals, peptides, and recombinant proteins Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich Cat#L2880 Pam3Cys EMC Microcollections Cat#L2000 Ficoll-Paque GE Healthcare Cat#17-1440-03 Percoll Sigma-Aldrich Cat#P1644 Protein A/G Magnetic beads Diagenode Cat#C03010021 b1,3-(D)glucan (b-glucan) 38 N/A Dimethylitaconate Sigma-Aldrich Cat#592498 Itaconate Sigma-Aldrich Cat#I29204 4-octyl itaconate 3 N/A Zymosan (fromS. cerevisiae) Sigma-Aldrich Cat#Z4250 MTA Sigma-Aldrich Cat#D5011 Oligomycin A Sigma-Aldrich Cat#75351 FCCP Sigma-Aldrich Cat#C2920 Antimycin A Sigma-Aldrich Cat#A8674 Rotenone Sigma-Aldrich Cat#R8875 2-DG Sigma-Aldrich Cat#D6134 MitoTempo Sigma-Aldrich Cat#SML0737 TMRE Sigma-Aldrich Cat#87917 H2DCFDA Life Technologies Cat#D399 MitoSOXTM Red Invitrogen Cat#M36008 Zymosan (from S. cerevisiae) Sigma-Aldrich Cat#Z4250 Luminol Sigma-Aldrich Cat#A8511 DPI Sigma-Aldrich Cat#D2926 NAC Sigma-Aldrich Cat#A7250 AT Sigma-Aldrich Cat#T3251 BSO Sigma-Aldrich Cat#B2515 Glutathione Monoethyl Ester Santa Cruz Biotechnology Cat#sc-203974 TRIzol Life Technologies Cat#15596018 Power SYBRTM Green PCR Master Mix Applied Biosystems Cat#4368708 Critical commercial assays Human TNFa ELISA R&D systems Cat#DY210 Human IL-6 ELISA R&D systems Cat#DY206 Human IL-1b ELISA R&D systems Cat#DY201 Human IL-10 ELISA R&D systems Cat#DY217B Human IL-1Ra ELISA R&D systems Cat#DY280 (Continued on next page) Cell Reports 42, 112658, June 27, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human IFNg ELISA R&D systems Cat#DY285B pHrodo Green S. aureus BioParticles ThermoFisher Scientific Cat#P35382 iScript cDNA Synthesis Kit Bio-Rad Cat#1708891 GSH/GSSG ratio detection assay kit Abcam Cat#ab138881 ATP assay kit Sigma-Aldrich Cat#MAK190 Pan Monocyte Isolation Kit Miltenyi Cat#130-096-537 PierceTM BCA Protein Assay Kit ThermoFisher Scientific Cat#23225 Deposited data RNA sequencing This study GEO: GSE212282 Experimental models: Organisms/strains Mouse: C57BL/6JOlaHsd Hellenic Pasteur Institute, Athens, Greece N/A Human: primary monocytes from healthy volunteers Sanquin Blood Bank N/A Human: primary monocytes from CGD patients and healthy volunteers This study N/A Human: 300BCG cohort 43,47,48 N/A Oligonucleotides Total of 26 oligonucleotides Sigma-Aldrich Table S1 Software and algorithms GraphPad Prism Graphpad Software https://www.graphpad.com Kaluza 2.1 Beckman Coulter https://www.beckman.com/ flow-cytometry/software/kaluza Bowtie 49 http://bowtie-bio.sourceforge.net/index. shtml MMSEQ 50 https://github.com/eturro/mmseq HOMER 51 http://homer.salk.edu/homer/motif R (information on used packages available upon request) N/A https://www.r-project.org/about.html Chenomx NMR suite 9.0 Chenomx https://www.chenomx.com/
Recombinant:Article Title: Dimethyl itaconate induces long-term innate immune responses and confers protection against infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BV785 anti-human CD11b antibody (ICRF44) Biolegend Cat#301346; RRID AB_2563794 Anti-H3K4me3 (polyclonal) Diagenode Cat#C15410003; RRID:AB_2924768 Anti-H3K9me3 (polyclonal) Diagenode Cat#C15410193; RRID:AB_2616044 Bacterial and virus strains Candida albicans (UC820 strain) ATCC ATCC MYA-3573 Staphylococcus aureus (RN4220 strain) 18 N/A Chemicals, peptides, and recombinant proteins Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich Cat#L2880 Pam3Cys EMC Microcollections Cat#L2000 Ficoll-Paque GE Healthcare Cat#17-1440-03 Percoll Sigma-Aldrich Cat#P1644 Protein A/G Magnetic beads Diagenode Cat#C03010021 b1,3-(D)glucan (b-glucan) 38 N/A Dimethylitaconate Sigma-Aldrich Cat#592498 Itaconate Sigma-Aldrich Cat#I29204 4-octyl itaconate 3 N/A Zymosan (fromS. cerevisiae) Sigma-Aldrich Cat#Z4250 MTA Sigma-Aldrich Cat#D5011 Oligomycin A Sigma-Aldrich Cat#75351 FCCP Sigma-Aldrich Cat#C2920 Antimycin A Sigma-Aldrich Cat#A8674 Rotenone Sigma-Aldrich Cat#R8875 2-DG Sigma-Aldrich Cat#D6134 MitoTempo Sigma-Aldrich Cat#SML0737 TMRE Sigma-Aldrich Cat#87917 H2DCFDA Life Technologies Cat#D399 MitoSOXTM Red Invitrogen Cat#M36008 Zymosan (from S. cerevisiae) Sigma-Aldrich Cat#Z4250 Luminol Sigma-Aldrich Cat#A8511 DPI Sigma-Aldrich Cat#D2926 NAC Sigma-Aldrich Cat#A7250 AT Sigma-Aldrich Cat#T3251 BSO Sigma-Aldrich Cat#B2515 Glutathione Monoethyl Ester Santa Cruz Biotechnology Cat#sc-203974 TRIzol Life Technologies Cat#15596018 Power SYBRTM Green PCR Master Mix Applied Biosystems Cat#4368708 Critical commercial assays Human TNFa ELISA R&D systems Cat#DY210 Human IL-6 ELISA R&D systems Cat#DY206 Human IL-1b ELISA R&D systems Cat#DY201 Human IL-10 ELISA R&D systems Cat#DY217B Human IL-1Ra ELISA R&D systems Cat#DY280 (Continued on next page) Cell Reports 42, 112658, June 27, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human IFNg ELISA R&D systems Cat#DY285B pHrodo Green S. aureus BioParticles ThermoFisher Scientific Cat#P35382 iScript cDNA Synthesis Kit Bio-Rad Cat#1708891 GSH/GSSG ratio detection assay kit Abcam Cat#ab138881 ATP assay kit Sigma-Aldrich Cat#MAK190 Pan Monocyte Isolation Kit Miltenyi Cat#130-096-537 PierceTM BCA Protein Assay Kit ThermoFisher Scientific Cat#23225 Deposited data RNA sequencing This study GEO: GSE212282 Experimental models: Organisms/strains Mouse: C57BL/6JOlaHsd Hellenic Pasteur Institute, Athens, Greece N/A Human: primary monocytes from healthy volunteers Sanquin Blood Bank N/A Human: primary monocytes from CGD patients and healthy volunteers This study N/A Human: 300BCG cohort 43,47,48 N/A Oligonucleotides Total of 26 oligonucleotides Sigma-Aldrich Table S1 Software and algorithms GraphPad Prism Graphpad Software https://www.graphpad.com Kaluza 2.1 Beckman Coulter https://www.beckman.com/ flow-cytometry/software/kaluza Bowtie 49 http://bowtie-bio.sourceforge.net/index. shtml MMSEQ 50 https://github.com/eturro/mmseq HOMER 51 http://homer.salk.edu/homer/motif R (information on used packages available upon request) N/A https://www.r-project.org/about.html Chenomx NMR suite 9.0 Chenomx https://www.chenomx.com/
Magnetic Beads:Article Title: Dimethyl itaconate induces long-term innate immune responses and confers protection against infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BV785 anti-human CD11b antibody (ICRF44) Biolegend Cat#301346; RRID AB_2563794 Anti-H3K4me3 (polyclonal) Diagenode Cat#C15410003; RRID:AB_2924768 Anti-H3K9me3 (polyclonal) Diagenode Cat#C15410193; RRID:AB_2616044 Bacterial and virus strains Candida albicans (UC820 strain) ATCC ATCC MYA-3573 Staphylococcus aureus (RN4220 strain) 18 N/A Chemicals, peptides, and recombinant proteins Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich Cat#L2880 Pam3Cys EMC Microcollections Cat#L2000 Ficoll-Paque GE Healthcare Cat#17-1440-03 Percoll Sigma-Aldrich Cat#P1644 Protein A/G Magnetic beads Diagenode Cat#C03010021 b1,3-(D)glucan (b-glucan) 38 N/A Dimethylitaconate Sigma-Aldrich Cat#592498 Itaconate Sigma-Aldrich Cat#I29204 4-octyl itaconate 3 N/A Zymosan (fromS. cerevisiae) Sigma-Aldrich Cat#Z4250 MTA Sigma-Aldrich Cat#D5011 Oligomycin A Sigma-Aldrich Cat#75351 FCCP Sigma-Aldrich Cat#C2920 Antimycin A Sigma-Aldrich Cat#A8674 Rotenone Sigma-Aldrich Cat#R8875 2-DG Sigma-Aldrich Cat#D6134 MitoTempo Sigma-Aldrich Cat#SML0737 TMRE Sigma-Aldrich Cat#87917 H2DCFDA Life Technologies Cat#D399 MitoSOXTM Red Invitrogen Cat#M36008 Zymosan (from S. cerevisiae) Sigma-Aldrich Cat#Z4250 Luminol Sigma-Aldrich Cat#A8511 DPI Sigma-Aldrich Cat#D2926 NAC Sigma-Aldrich Cat#A7250 AT Sigma-Aldrich Cat#T3251 BSO Sigma-Aldrich Cat#B2515 Glutathione Monoethyl Ester Santa Cruz Biotechnology Cat#sc-203974 TRIzol Life Technologies Cat#15596018 Power SYBRTM Green PCR Master Mix Applied Biosystems Cat#4368708 Critical commercial assays Human TNFa ELISA R&D systems Cat#DY210 Human IL-6 ELISA R&D systems Cat#DY206 Human IL-1b ELISA R&D systems Cat#DY201 Human IL-10 ELISA R&D systems Cat#DY217B Human IL-1Ra ELISA R&D systems Cat#DY280 (Continued on next page) Cell Reports 42, 112658, June 27, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human IFNg ELISA R&D systems Cat#DY285B pHrodo Green S. aureus BioParticles ThermoFisher Scientific Cat#P35382 iScript cDNA Synthesis Kit Bio-Rad Cat#1708891 GSH/GSSG ratio detection assay kit Abcam Cat#ab138881 ATP assay kit Sigma-Aldrich Cat#MAK190 Pan Monocyte Isolation Kit Miltenyi Cat#130-096-537 PierceTM BCA Protein Assay Kit ThermoFisher Scientific Cat#23225 Deposited data RNA sequencing This study GEO: GSE212282 Experimental models: Organisms/strains Mouse: C57BL/6JOlaHsd Hellenic Pasteur Institute, Athens, Greece N/A Human: primary monocytes from healthy volunteers Sanquin Blood Bank N/A Human: primary monocytes from CGD patients and healthy volunteers This study N/A Human: 300BCG cohort 43,47,48 N/A Oligonucleotides Total of 26 oligonucleotides Sigma-Aldrich Table S1 Software and algorithms GraphPad Prism Graphpad Software https://www.graphpad.com Kaluza 2.1 Beckman Coulter https://www.beckman.com/ flow-cytometry/software/kaluza Bowtie 49 http://bowtie-bio.sourceforge.net/index. shtml MMSEQ 50 https://github.com/eturro/mmseq HOMER 51 http://homer.salk.edu/homer/motif R (information on used packages available upon request) N/A https://www.r-project.org/about.html Chenomx NMR suite 9.0 Chenomx https://www.chenomx.com/
Polymerase Chain Reaction:Article Title: Dimethyl itaconate induces long-term innate immune responses and confers protection against infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BV785 anti-human CD11b antibody (ICRF44) Biolegend Cat#301346; RRID AB_2563794 Anti-H3K4me3 (polyclonal) Diagenode Cat#C15410003; RRID:AB_2924768 Anti-H3K9me3 (polyclonal) Diagenode Cat#C15410193; RRID:AB_2616044 Bacterial and virus strains Candida albicans (UC820 strain) ATCC ATCC MYA-3573 Staphylococcus aureus (RN4220 strain) 18 N/A Chemicals, peptides, and recombinant proteins Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich Cat#L2880 Pam3Cys EMC Microcollections Cat#L2000 Ficoll-Paque GE Healthcare Cat#17-1440-03 Percoll Sigma-Aldrich Cat#P1644 Protein A/G Magnetic beads Diagenode Cat#C03010021 b1,3-(D)glucan (b-glucan) 38 N/A Dimethylitaconate Sigma-Aldrich Cat#592498 Itaconate Sigma-Aldrich Cat#I29204 4-octyl itaconate 3 N/A Zymosan (fromS. cerevisiae) Sigma-Aldrich Cat#Z4250 MTA Sigma-Aldrich Cat#D5011 Oligomycin A Sigma-Aldrich Cat#75351 FCCP Sigma-Aldrich Cat#C2920 Antimycin A Sigma-Aldrich Cat#A8674 Rotenone Sigma-Aldrich Cat#R8875 2-DG Sigma-Aldrich Cat#D6134 MitoTempo Sigma-Aldrich Cat#SML0737 TMRE Sigma-Aldrich Cat#87917 H2DCFDA Life Technologies Cat#D399 MitoSOXTM Red Invitrogen Cat#M36008 Zymosan (from S. cerevisiae) Sigma-Aldrich Cat#Z4250 Luminol Sigma-Aldrich Cat#A8511 DPI Sigma-Aldrich Cat#D2926 NAC Sigma-Aldrich Cat#A7250 AT Sigma-Aldrich Cat#T3251 BSO Sigma-Aldrich Cat#B2515 Glutathione Monoethyl Ester Santa Cruz Biotechnology Cat#sc-203974 TRIzol Life Technologies Cat#15596018 Power SYBRTM Green PCR Master Mix Applied Biosystems Cat#4368708 Critical commercial assays Human TNFa ELISA R&D systems Cat#DY210 Human IL-6 ELISA R&D systems Cat#DY206 Human IL-1b ELISA R&D systems Cat#DY201 Human IL-10 ELISA R&D systems Cat#DY217B Human IL-1Ra ELISA R&D systems Cat#DY280 (Continued on next page) Cell Reports 42, 112658, June 27, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human IFNg ELISA R&D systems Cat#DY285B pHrodo Green S. aureus BioParticles ThermoFisher Scientific Cat#P35382 iScript cDNA Synthesis Kit Bio-Rad Cat#1708891 GSH/GSSG ratio detection assay kit Abcam Cat#ab138881 ATP assay kit Sigma-Aldrich Cat#MAK190 Pan Monocyte Isolation Kit Miltenyi Cat#130-096-537 PierceTM BCA Protein Assay Kit ThermoFisher Scientific Cat#23225 Deposited data RNA sequencing This study GEO: GSE212282 Experimental models: Organisms/strains Mouse: C57BL/6JOlaHsd Hellenic Pasteur Institute, Athens, Greece N/A Human: primary monocytes from healthy volunteers Sanquin Blood Bank N/A Human: primary monocytes from CGD patients and healthy volunteers This study N/A Human: 300BCG cohort 43,47,48 N/A Oligonucleotides Total of 26 oligonucleotides Sigma-Aldrich Table S1 Software and algorithms GraphPad Prism Graphpad Software https://www.graphpad.com Kaluza 2.1 Beckman Coulter https://www.beckman.com/ flow-cytometry/software/kaluza Bowtie 49 http://bowtie-bio.sourceforge.net/index. shtml MMSEQ 50 https://github.com/eturro/mmseq HOMER 51 http://homer.salk.edu/homer/motif R (information on used packages available upon request) N/A https://www.r-project.org/about.html Chenomx NMR suite 9.0 Chenomx https://www.chenomx.com/
Enzyme-linked Immunosorbent Assay:Article Title: Dimethyl itaconate induces long-term innate immune responses and confers protection against infection.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies BV785 anti-human CD11b antibody (ICRF44) Biolegend Cat#301346; RRID AB_2563794 Anti-H3K4me3 (polyclonal) Diagenode Cat#C15410003; RRID:AB_2924768 Anti-H3K9me3 (polyclonal) Diagenode Cat#C15410193; RRID:AB_2616044 Bacterial and virus strains Candida albicans (UC820 strain) ATCC ATCC MYA-3573 Staphylococcus aureus (RN4220 strain) 18 N/A Chemicals, peptides, and recombinant proteins Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich Cat#L2880 Pam3Cys EMC Microcollections Cat#L2000 Ficoll-Paque GE Healthcare Cat#17-1440-03 Percoll Sigma-Aldrich Cat#P1644 Protein A/G Magnetic beads Diagenode Cat#C03010021 b1,3-(D)glucan (b-glucan) 38 N/A Dimethylitaconate Sigma-Aldrich Cat#592498 Itaconate Sigma-Aldrich Cat#I29204 4-octyl itaconate 3 N/A Zymosan (fromS. cerevisiae) Sigma-Aldrich Cat#Z4250 MTA Sigma-Aldrich Cat#D5011 Oligomycin A Sigma-Aldrich Cat#75351 FCCP Sigma-Aldrich Cat#C2920 Antimycin A Sigma-Aldrich Cat#A8674 Rotenone Sigma-Aldrich Cat#R8875 2-DG Sigma-Aldrich Cat#D6134 MitoTempo Sigma-Aldrich Cat#SML0737 TMRE Sigma-Aldrich Cat#87917 H2DCFDA Life Technologies Cat#D399 MitoSOXTM Red Invitrogen Cat#M36008 Zymosan (from S. cerevisiae) Sigma-Aldrich Cat#Z4250 Luminol Sigma-Aldrich Cat#A8511 DPI Sigma-Aldrich Cat#D2926 NAC Sigma-Aldrich Cat#A7250 AT Sigma-Aldrich Cat#T3251 BSO Sigma-Aldrich Cat#B2515 Glutathione Monoethyl Ester Santa Cruz Biotechnology Cat#sc-203974 TRIzol Life Technologies Cat#15596018 Power SYBRTM Green PCR Master Mix Applied Biosystems Cat#4368708 Critical commercial assays Human TNFa ELISA R&D systems Cat#DY210 Human IL-6 ELISA R&D systems Cat#DY206 Human IL-1b ELISA R&D systems Cat#DY201 Human IL-10 ELISA R&D systems Cat#DY217B Human IL-1Ra ELISA R&D systems Cat#DY280 (Continued on next page) Cell Reports 42, 112658, June 27, 2023 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Human IFNg ELISA R&D systems Cat#DY285B pHrodo Green S. aureus BioParticles ThermoFisher Scientific Cat#P35382 iScript cDNA Synthesis Kit Bio-Rad Cat#1708891 GSH/GSSG ratio detection assay kit Abcam Cat#ab138881 ATP assay kit Sigma-Aldrich Cat#MAK190 Pan Monocyte Isolation Kit Miltenyi Cat#130-096-537 PierceTM BCA Protein Assay Kit ThermoFisher Scientific Cat#23225 Deposited data RNA sequencing This study GEO: GSE212282 Experimental models: Organisms/strains Mouse: C57BL/6JOlaHsd Hellenic Pasteur Institute, Athens, Greece N/A Human: primary monocytes from healthy volunteers Sanquin Blood Bank N/A Human: primary monocytes from CGD patients and healthy volunteers This study N/A Human: 300BCG cohort 43,47,48 N/A Oligonucleotides Total of 26 oligonucleotides Sigma-Aldrich Table S1 Software and algorithms GraphPad Prism Graphpad Software https://www.graphpad.com Kaluza 2.1 Beckman Coulter https://www.beckman.com/ flow-cytometry/software/kaluza Bowtie 49 http://bowtie-bio.sourceforge.net/index. shtml MMSEQ 50 https://github.com/eturro/mmseq HOMER 51 http://homer.salk.edu/homer/motif R (information on used packages available upon request) N/A https://www.r-project.org/about.html Chenomx NMR suite 9.0 Chenomx https://www.chenomx.com/
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