Recombinant:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
Nick Translation:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
DNA Labeling:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
In Situ:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
Mass Spectrometry:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
Targeted Proteomics:Article Title: Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Topo IIbeta (H-8) Santa Cruz RRID: AB_628384 Topo IIbeta Abcam RRID: AB_2923318 Pan-Calcineurin A Antibody Cell Signaling Technology RRID: AB_2168458 Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 MilliporeSigma RRID: AB_309864 Calcineurin A Polyclonal Antibody Thermo Fisher Scientific RRID: AB_10981308 Histone H2A.X antibody Abcam RRID: AB_297814 Goat Anti-Rabbit IgG Antibody, IRDye 800CW LI-COR RRID: AB_10796098 Lamin A/C (4C11) Mouse mAb (Alexa Fluor 488 Conjugate) Cell Signaling Technology RRID: AB_10997529 Phospho-Topoisomerase IIa (Ser, 1469) (D4F5) Cell Signaling Technology RRID: AB_2798109 Phospho-CK2 Substrate [(pS/pT) DXE] MultiMab Cell Signaling Technology RRID: AB_2797653 Goat anti-Mouse IgG (H + L) Antibody, IRDye 680RD LI-COR RRID: AB_10956589 Actin beta Bio-Rad RRID: AB_2923317 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534091 Goat anti-Rabbit IgG (H+L) Highly CrossAdsorbed Secondary Antibody, Alexa Fluor 594 Thermo Fisher Scientific RRID:AB_2534095 Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535805 Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 647 Thermo Fisher Scientific RRID:AB_2535813 Lamin A/C Cell Signaling Technology RRID:AB_10545756 Anti-gamma H2A.X (phospho S139) antibody Abcam RRID:AB_303388 Chemicals, peptides, and recombinant proteins Recombinant Human Calcineurin Protein R&D systems Cat#3160-CA Calmodulin (Human) (recombinant) Enzo Cat#BML-SE325-0001 Recombinant Human Topoisomerase II beta/TOP2B protein Abcam Cat#ab159736 KN-62 MilliporeSigma Cat#422706-1MG KT5720 MilliporeSigma Cat#420323-50UG Dantrolene, sodium salt Tocris Cat#0507 InSolution Okadaic Acid, Prorocentrum MilliporeSigma Cat#495609-25UG Nifedipine Tocris Cat#1075 2 aminoethoxydiphenyl borate (2APB) Tocris Cat#1224 MEK/ERK inhibitor Tocris CatPD98059 Calcineurin Inhibitor VIII, CN585 - MilliporeSigma Cat#207003-10MG Tacrolimus (FK506) Selleckchem Cat#S5003 D-AP5 Tocris Cat#0106 Critical commercial assays Nick Translation DNA Labeling System ENZO Cat#ENZ-GEN111-0050 Duolink In Situ Detection Reagents FarRed MilliporeSigma Cat# DUO92013 Deposited data Targeted Mass Spectrometry (PRM LC – MS/MS) This paper MassIVE: MSV000088392 (Continued on next page) e1 Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 .. REAGENT or RESOURCE SOURCE IDENTIFIER Mass Spectrometry (LC – MS/MS of immunoprecipitated Top2B) This paper MassIVE: MSV000089825 Mendeley Dataset - Unprocessed blots, gels, and microscopy images This paper DOI: Experimental models: Cell lines NIH 3T3 ATCC Cat#CVCL_0594 HEK293 ATCC Cat#CVCL_0045 Experimental models: Organisms/strains Mouse C57BL/6J The Jackson Laboratory Cat#000664 Oligonucleotides Fos Exon Forward: GCCAACTTTATCCCCACGGT N/A Fos Exon Reverse: TCTTCACCATTCCCGCTCTG (Madabhushi et al., 2015) N/A Npas4 Exon Forward: GAGCAAGAGCCTGAGCGAAAAG (Madabhushi et al., 2015) N/A Npas4 Exon Reverse: CCAGCAAAGAAGACACCCTTG (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A bglobin Forward: TGACCAATAGTCTCGGAGTCCTG (Madabhushi et al., 2015) N/A bglobin Reverse: AGGCTGAAGGCCTGTCCTTT (Madabhushi et al., 2015) N/A Fos Forward: GAACGGAATAAGATGGCTGC (Madabhushi et al., 2015) N/A Fos Reverse: TTGATCTGTCTCCGCTTGG (Madabhushi et al., 2015) N/A FosB Forward: CCCGAGAAGAGACACTTACC (Madabhushi et al., 2015) N/A FosB Reverse: CTCTTCAAGCTGATCAGTTTCC (Madabhushi et al., 2015) N/A Npas4 Forward: CTGCATCTACACTCGCAAGG (Madabhushi et al., 2015) N/A Npas4 Reverse: GCCACAATGTCTTCAAGCTCT (Madabhushi et al., 2015) N/A Egr1 Forward: AGCGAACAACCCTATGAGCA (Madabhushi et al., 2015) N/A Egr1 Reverse: TCGTTTGGCTGGGATAACTC (Madabhushi et al., 2015) N/A GAPDH Forward: CTCTCCTCCTCCCTGTTCC (Madabhushi et al., 2015) N/A GAPDH Reverse: TCCCTAGACCCGTACAGTGC (Madabhushi et al., 2015) N/A Nr4a1 Forward: ATGCCTCCCCTACCAATCTTC (Madabhushi et al., 2015) N/A Nr4a1 Reverse: CACCAGTTCCTGGAACTTGGA (Madabhushi et al., 2015) N/A ActB Forward: GGCTGTATTCCCCTCCATCG (Madabhushi et al., 2015) N/A ActB Reverse: CCAGTTGGTAACAATGCCATGT (Madabhushi et al., 2015) N/A HA-tagged mouse DNA topoisomerase IIb Addgene Cat# pYLL201 Recombinant DNA and viral particles Fos CHORI (Children’s Hospital Oakland Research Institute) RP24-208N11 Fos (upstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-368B17 Fos (downstream) CHORI (Children’s Hospital Oakland Research Institute) RP24-178I11 FosB CHORI (Children’s Hospital Oakland Research Institute) RP24-161J12 ActB CHORI (Children’s Hospital Oakland Research Institute) RP24-266N Malat1 CHORI (Children’s Hospital Oakland Research Institute) RP24-290K10 Npas4 CHORI (Children’s Hospital Oakland Research Institute) RP24-238I5 Gm50442 CHORI (Children’s Hospital Oakland Research Institute) RP24-344E18 AAV-hSyn-GFP-Cre virus serotype 8 UNC Vector Core N/A Molecular Cell 82, 3794–3809.e1–e8, October 20, 2022 e2
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