Recombinant:Article Title: The basic domain of Suv39h2 buffers mitoxantrone-induced heterochromatin destabilization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies goat polyclonal α-GFP Rockland Cat#: 600-141-215; RRID: AB_1961516 rabbit polyclonal α-GFP Invitrogen Cat#: A11122; RRID: AB_221569 mouse monoclonal α-GAPDH SantaCruz Biotechnology Cat#: sc-32233; RRID: AB_627679 rabbit monoclonal α-HP1α Abcam Cat#: ab109028; RRID: AB_10858495 rabbit polyclonal α-H3K9me3 Abcam Cat#: 8898; RRID: AB_306848 mouse polyclonal α-H2A.X (Ser139) Millipore Cat#: 05-636; RRID: AB_309864 rabbit monoclonal α-H3 Abcam Cat#: ab176842; RRID: AB_2493104 rabbit polyclonal α-H3K9me3 Jenuwein lab # 1926 mouse monoclonal α-Nucleophosmin Abcam Cat#: ab10530; RRID: AB_297271 Chemicals, peptides, and recombinant proteins High-glucose Dulbecco’s Modified Eagle Medium (DMEM) Sigma-Aldrich Cat#: D6171 HyClone Characterized Fetal bovine serum Cytiva Cat#: SH30071.03 L-glutamine Sigma-Aldrich Cat#: G7513 β-mercaptoethanol Gibco Cat#: 31350-010 MEM Non-essential Amino Acid Solution (100×) Sigma-Aldrich Cat#: M7145 sodium pyruvate solution Sigma-Aldrich Cat#: S8636 penicillin-streptomycin Sigma-Aldrich Cat#: P4333 puromycin dihydrochloride Sigma-Aldrich Cat#: P9620 XhoI restriction enzyme New England Biolabs Cat#: R0146S AflII restriction enzyme New England Biolabs Cat#: R05020S PvuI restriction enzyme New England Biolabs Cat#: R3150S XFect Transfection reagent Takara Cat#: 631317 DPBS Gibco Cat#: 14190-094 RIPA Pierce Cat#: 89900 cOmplete EDTA-free protease inhibitors Roche Cat#: 11873580001 paraformaldehyde Santa Cruz Cat#: sc-281692 triton X-100 Sigma-Aldrich Cat#: X100 VECTASHIELD Antifade Mounting Medium with DAPI Vector Leboratories Cat#: H-1200 donkey serum Jackson ImmunoResearch Cat#: 017-000-121 phenol red-free DMEM Gibco Cat#: 21063029 1,6-hexanediol Sigma-Aldrich Cat#: 240117 low melting point agarose Bethesda Scientific Cat#: V3841 RNaseA Thermo Scientific Cat#: EN0531 mitoxantrone Selleckchem Cat#: S2485 cbl-0137 Selleckchem Cat#: S0507 formaldehyde Sigma-Aldrich Cat#: F8775 glycine Sigma-Aldrich Cat#: G8898 SDS Sigma-Aldrich Cat#: L3771 EDTA Sigma-Aldrich Cat#: 798681 tris-HCl Sigma-Aldrich Cat#: 108315 (Continued on next page) iScience 29, 115626, May 15, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat#: S5886 dynabeads Protein G for Immunoprecipitation Invitrogen Cat#: 10003D LiCl Merck Cat#: 310468 sodium deoxycholate Sigma-Aldrich Cat#: D6750 NaHCO3 Merck Cat#: S6297 proteinase K Thermo Scientific Cat#: EO0491 MNase Thermo Scientific Cat#: EN0181 SYBR Select Master Mix Applied Biosystems Cat#: 4472908 SYBR Safe DNA Gel Stain Invitrogen Cat#: S33102 HEPES Merck Cat#: H3375 MgCl2 Merck Cat#: M8266 CaCl2 Merck Cat#:449709 Critical commercial assays NucleoSpin Gel and PCR Clean-up Kit Macherey-Nagel Cat#: 740609.250 Deposited data Original western blot images Mendeley: https://doi.org/10.17632/ wccscb4vt3.1 N/A Experimental models: Cell lines W8 immortalized mouse embryonic fibroblasts Jenuwein lab W8 D5 immortalized mouse embryonic fibroblasts Jenuwein lab D5 NIH 3T3 HP1α-EGFP immortalized mouse embryonic fibroblasts Jenuwein lab N/A Oligonucleotides MSR_for (5’-TGGAATATGGC GAGAAAACTG) Ching et al.73 N/A MSR_rev (5’-AGGTCCTTCAG TGGGCATTT) Ching et al.73 N/A Recombinant DNA pCAGGS-Suv39h1-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #693 pCAGGS-Suv39h2-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #694 pCAGGS-Suv39h2ΔBD-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #703 pCAGGS-BD-Suv39h1-EGFP-IRES-Puro This study Laboratory of Thomas Jenuwein Database: #696 Software and algorithms R (v4.4.3) R Core Team https://www.r-project.org/ Clustal Omega EMBL-EBI https://www.ebi.ac.uk/Tools/msa/clustalo/ GraphPad Prism 10 GraphPad Software https://www.graphpad.com/ Peptides (v2.4.6) Charif & Lobry, 2007 https://cran.r-project.org/package=Peptides ggplot2 (v3.5.1) Hadley Wickham https://cran.r-project.org/package=ggplot2 ggrepel (v0.9.6) Slowikowski et al. https://cran.r-project.org/package=ggrepel IUPred2 Dosztányi et al., 2005 https://iupred2a.elte.hu/ Zen Black software Zeiss https://www.zeiss.com/microscopy/ int/products/microscope-software/zen.html Fiji (v2.9.0) Schindelin et al., 2012 https://fiji.sc/ Marvin JS (22.11.1) Chemaxon internal http://www.chemaxon.com e2 iScience 29, 115626, May 15, 2026
Modification:Article Title: The basic domain of Suv39h2 buffers mitoxantrone-induced heterochromatin destabilization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies goat polyclonal α-GFP Rockland Cat#: 600-141-215; RRID: AB_1961516 rabbit polyclonal α-GFP Invitrogen Cat#: A11122; RRID: AB_221569 mouse monoclonal α-GAPDH SantaCruz Biotechnology Cat#: sc-32233; RRID: AB_627679 rabbit monoclonal α-HP1α Abcam Cat#: ab109028; RRID: AB_10858495 rabbit polyclonal α-H3K9me3 Abcam Cat#: 8898; RRID: AB_306848 mouse polyclonal α-H2A.X (Ser139) Millipore Cat#: 05-636; RRID: AB_309864 rabbit monoclonal α-H3 Abcam Cat#: ab176842; RRID: AB_2493104 rabbit polyclonal α-H3K9me3 Jenuwein lab # 1926 mouse monoclonal α-Nucleophosmin Abcam Cat#: ab10530; RRID: AB_297271 Chemicals, peptides, and recombinant proteins High-glucose Dulbecco’s Modified Eagle Medium (DMEM) Sigma-Aldrich Cat#: D6171 HyClone Characterized Fetal bovine serum Cytiva Cat#: SH30071.03 L-glutamine Sigma-Aldrich Cat#: G7513 β-mercaptoethanol Gibco Cat#: 31350-010 MEM Non-essential Amino Acid Solution (100×) Sigma-Aldrich Cat#: M7145 sodium pyruvate solution Sigma-Aldrich Cat#: S8636 penicillin-streptomycin Sigma-Aldrich Cat#: P4333 puromycin dihydrochloride Sigma-Aldrich Cat#: P9620 XhoI restriction enzyme New England Biolabs Cat#: R0146S AflII restriction enzyme New England Biolabs Cat#: R05020S PvuI restriction enzyme New England Biolabs Cat#: R3150S XFect Transfection reagent Takara Cat#: 631317 DPBS Gibco Cat#: 14190-094 RIPA Pierce Cat#: 89900 cOmplete EDTA-free protease inhibitors Roche Cat#: 11873580001 paraformaldehyde Santa Cruz Cat#: sc-281692 triton X-100 Sigma-Aldrich Cat#: X100 VECTASHIELD Antifade Mounting Medium with DAPI Vector Leboratories Cat#: H-1200 donkey serum Jackson ImmunoResearch Cat#: 017-000-121 phenol red-free DMEM Gibco Cat#: 21063029 1,6-hexanediol Sigma-Aldrich Cat#: 240117 low melting point agarose Bethesda Scientific Cat#: V3841 RNaseA Thermo Scientific Cat#: EN0531 mitoxantrone Selleckchem Cat#: S2485 cbl-0137 Selleckchem Cat#: S0507 formaldehyde Sigma-Aldrich Cat#: F8775 glycine Sigma-Aldrich Cat#: G8898 SDS Sigma-Aldrich Cat#: L3771 EDTA Sigma-Aldrich Cat#: 798681 tris-HCl Sigma-Aldrich Cat#: 108315 (Continued on next page) iScience 29, 115626, May 15, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat#: S5886 dynabeads Protein G for Immunoprecipitation Invitrogen Cat#: 10003D LiCl Merck Cat#: 310468 sodium deoxycholate Sigma-Aldrich Cat#: D6750 NaHCO3 Merck Cat#: S6297 proteinase K Thermo Scientific Cat#: EO0491 MNase Thermo Scientific Cat#: EN0181 SYBR Select Master Mix Applied Biosystems Cat#: 4472908 SYBR Safe DNA Gel Stain Invitrogen Cat#: S33102 HEPES Merck Cat#: H3375 MgCl2 Merck Cat#: M8266 CaCl2 Merck Cat#:449709 Critical commercial assays NucleoSpin Gel and PCR Clean-up Kit Macherey-Nagel Cat#: 740609.250 Deposited data Original western blot images Mendeley: https://doi.org/10.17632/ wccscb4vt3.1 N/A Experimental models: Cell lines W8 immortalized mouse embryonic fibroblasts Jenuwein lab W8 D5 immortalized mouse embryonic fibroblasts Jenuwein lab D5 NIH 3T3 HP1α-EGFP immortalized mouse embryonic fibroblasts Jenuwein lab N/A Oligonucleotides MSR_for (5’-TGGAATATGGC GAGAAAACTG) Ching et al.73 N/A MSR_rev (5’-AGGTCCTTCAG TGGGCATTT) Ching et al.73 N/A Recombinant DNA pCAGGS-Suv39h1-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #693 pCAGGS-Suv39h2-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #694 pCAGGS-Suv39h2ΔBD-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #703 pCAGGS-BD-Suv39h1-EGFP-IRES-Puro This study Laboratory of Thomas Jenuwein Database: #696 Software and algorithms R (v4.4.3) R Core Team https://www.r-project.org/ Clustal Omega EMBL-EBI https://www.ebi.ac.uk/Tools/msa/clustalo/ GraphPad Prism 10 GraphPad Software https://www.graphpad.com/ Peptides (v2.4.6) Charif & Lobry, 2007 https://cran.r-project.org/package=Peptides ggplot2 (v3.5.1) Hadley Wickham https://cran.r-project.org/package=ggplot2 ggrepel (v0.9.6) Slowikowski et al. https://cran.r-project.org/package=ggrepel IUPred2 Dosztányi et al., 2005 https://iupred2a.elte.hu/ Zen Black software Zeiss https://www.zeiss.com/microscopy/ int/products/microscope-software/zen.html Fiji (v2.9.0) Schindelin et al., 2012 https://fiji.sc/ Marvin JS (22.11.1) Chemaxon internal http://www.chemaxon.com e2 iScience 29, 115626, May 15, 2026
Transfection:Article Title: The basic domain of Suv39h2 buffers mitoxantrone-induced heterochromatin destabilization.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies goat polyclonal α-GFP Rockland Cat#: 600-141-215; RRID: AB_1961516 rabbit polyclonal α-GFP Invitrogen Cat#: A11122; RRID: AB_221569 mouse monoclonal α-GAPDH SantaCruz Biotechnology Cat#: sc-32233; RRID: AB_627679 rabbit monoclonal α-HP1α Abcam Cat#: ab109028; RRID: AB_10858495 rabbit polyclonal α-H3K9me3 Abcam Cat#: 8898; RRID: AB_306848 mouse polyclonal α-H2A.X (Ser139) Millipore Cat#: 05-636; RRID: AB_309864 rabbit monoclonal α-H3 Abcam Cat#: ab176842; RRID: AB_2493104 rabbit polyclonal α-H3K9me3 Jenuwein lab # 1926 mouse monoclonal α-Nucleophosmin Abcam Cat#: ab10530; RRID: AB_297271 Chemicals, peptides, and recombinant proteins High-glucose Dulbecco’s Modified Eagle Medium (DMEM) Sigma-Aldrich Cat#: D6171 HyClone Characterized Fetal bovine serum Cytiva Cat#: SH30071.03 L-glutamine Sigma-Aldrich Cat#: G7513 β-mercaptoethanol Gibco Cat#: 31350-010 MEM Non-essential Amino Acid Solution (100×) Sigma-Aldrich Cat#: M7145 sodium pyruvate solution Sigma-Aldrich Cat#: S8636 penicillin-streptomycin Sigma-Aldrich Cat#: P4333 puromycin dihydrochloride Sigma-Aldrich Cat#: P9620 XhoI restriction enzyme New England Biolabs Cat#: R0146S AflII restriction enzyme New England Biolabs Cat#: R05020S PvuI restriction enzyme New England Biolabs Cat#: R3150S XFect Transfection reagent Takara Cat#: 631317 DPBS Gibco Cat#: 14190-094 RIPA Pierce Cat#: 89900 cOmplete EDTA-free protease inhibitors Roche Cat#: 11873580001 paraformaldehyde Santa Cruz Cat#: sc-281692 triton X-100 Sigma-Aldrich Cat#: X100 VECTASHIELD Antifade Mounting Medium with DAPI Vector Leboratories Cat#: H-1200 donkey serum Jackson ImmunoResearch Cat#: 017-000-121 phenol red-free DMEM Gibco Cat#: 21063029 1,6-hexanediol Sigma-Aldrich Cat#: 240117 low melting point agarose Bethesda Scientific Cat#: V3841 RNaseA Thermo Scientific Cat#: EN0531 mitoxantrone Selleckchem Cat#: S2485 cbl-0137 Selleckchem Cat#: S0507 formaldehyde Sigma-Aldrich Cat#: F8775 glycine Sigma-Aldrich Cat#: G8898 SDS Sigma-Aldrich Cat#: L3771 EDTA Sigma-Aldrich Cat#: 798681 tris-HCl Sigma-Aldrich Cat#: 108315 (Continued on next page) iScience 29, 115626, May 15, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER NaCl Sigma-Aldrich Cat#: S5886 dynabeads Protein G for Immunoprecipitation Invitrogen Cat#: 10003D LiCl Merck Cat#: 310468 sodium deoxycholate Sigma-Aldrich Cat#: D6750 NaHCO3 Merck Cat#: S6297 proteinase K Thermo Scientific Cat#: EO0491 MNase Thermo Scientific Cat#: EN0181 SYBR Select Master Mix Applied Biosystems Cat#: 4472908 SYBR Safe DNA Gel Stain Invitrogen Cat#: S33102 HEPES Merck Cat#: H3375 MgCl2 Merck Cat#: M8266 CaCl2 Merck Cat#:449709 Critical commercial assays NucleoSpin Gel and PCR Clean-up Kit Macherey-Nagel Cat#: 740609.250 Deposited data Original western blot images Mendeley: https://doi.org/10.17632/ wccscb4vt3.1 N/A Experimental models: Cell lines W8 immortalized mouse embryonic fibroblasts Jenuwein lab W8 D5 immortalized mouse embryonic fibroblasts Jenuwein lab D5 NIH 3T3 HP1α-EGFP immortalized mouse embryonic fibroblasts Jenuwein lab N/A Oligonucleotides MSR_for (5’-TGGAATATGGC GAGAAAACTG) Ching et al.73 N/A MSR_rev (5’-AGGTCCTTCAG TGGGCATTT) Ching et al.73 N/A Recombinant DNA pCAGGS-Suv39h1-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #693 pCAGGS-Suv39h2-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #694 pCAGGS-Suv39h2ΔBD-EGFP-IRES-Puro Velazquez et al.8 Laboratory of Thomas Jenuwein Database: #703 pCAGGS-BD-Suv39h1-EGFP-IRES-Puro This study Laboratory of Thomas Jenuwein Database: #696 Software and algorithms R (v4.4.3) R Core Team https://www.r-project.org/ Clustal Omega EMBL-EBI https://www.ebi.ac.uk/Tools/msa/clustalo/ GraphPad Prism 10 GraphPad Software https://www.graphpad.com/ Peptides (v2.4.6) Charif & Lobry, 2007 https://cran.r-project.org/package=Peptides ggplot2 (v3.5.1) Hadley Wickham https://cran.r-project.org/package=ggplot2 ggrepel (v0.9.6) Slowikowski et al. https://cran.r-project.org/package=ggrepel IUPred2 Dosztányi et al., 2005 https://iupred2a.elte.hu/ Zen Black software Zeiss https://www.zeiss.com/microscopy/ int/products/microscope-software/zen.html Fiji (v2.9.0) Schindelin et al., 2012 https://fiji.sc/ Marvin JS (22.11.1) Chemaxon internal http://www.chemaxon.com e2 iScience 29, 115626, May 15, 2026
Mutagenesis:Article Title: OptoLoop – an optogenetic tool to probe the functional role of genome organization
Article Snippet: .. A list of all plasmids with their corresponding sources can be found in . pCMV-CRY2hiclu-mCherry was obtained by replacing residues 504–507 from pCMV-CRY2high-mCherry by Asp-Leu-Asp-Asn via site-directed mutagenesis with the Q5 Site-Directed Mutagenesis kit (New England Biolabs, Ipswich, MA, USA). pHAGE-dCas9-mCherry-CRY2 was generated by replacing 2XmCherry in pHAGE-dCas9-3XmCh with PCR-amplified CRY2hiclu using NotI/XhoI sites. pHAGE-dCas9-3XmCherry-CRY2 and pHAGE-dCas9-3XGFP-CRY2 were generated with the NEB HiFi DNA assembly kit (New England Biolabs, Ipswich, MA, USA) by inserting PCR-amplified CRY2hiclu in XhoI-linearized pHAGE-dCas9-3XmCh and pHAGE-dCas9-3XGFP, respectively. pHAGE-dCas9-3XGFP-CIBN was generated by inserting PCR-amplified CIBN from pEF1a-dCas9-CIBN in pHAGE-dCas9-3XGFP using XhoI/Xba sites. .. All plasmid constructs generated in this work were verified by whole-plasmid sequencing and deposited in Addgene (see ).
Generated:Article Title: OptoLoop – an optogenetic tool to probe the functional role of genome organization
Article Snippet: .. A list of all plasmids with their corresponding sources can be found in . pCMV-CRY2hiclu-mCherry was obtained by replacing residues 504–507 from pCMV-CRY2high-mCherry by Asp-Leu-Asp-Asn via site-directed mutagenesis with the Q5 Site-Directed Mutagenesis kit (New England Biolabs, Ipswich, MA, USA). pHAGE-dCas9-mCherry-CRY2 was generated by replacing 2XmCherry in pHAGE-dCas9-3XmCh with PCR-amplified CRY2hiclu using NotI/XhoI sites. pHAGE-dCas9-3XmCherry-CRY2 and pHAGE-dCas9-3XGFP-CRY2 were generated with the NEB HiFi DNA assembly kit (New England Biolabs, Ipswich, MA, USA) by inserting PCR-amplified CRY2hiclu in XhoI-linearized pHAGE-dCas9-3XmCh and pHAGE-dCas9-3XGFP, respectively. pHAGE-dCas9-3XGFP-CIBN was generated by inserting PCR-amplified CIBN from pEF1a-dCas9-CIBN in pHAGE-dCas9-3XGFP using XhoI/Xba sites. .. All plasmid constructs generated in this work were verified by whole-plasmid sequencing and deposited in Addgene (see ).
Polymerase Chain Reaction:Article Title: OptoLoop – an optogenetic tool to probe the functional role of genome organization
Article Snippet: .. A list of all plasmids with their corresponding sources can be found in . pCMV-CRY2hiclu-mCherry was obtained by replacing residues 504–507 from pCMV-CRY2high-mCherry by Asp-Leu-Asp-Asn via site-directed mutagenesis with the Q5 Site-Directed Mutagenesis kit (New England Biolabs, Ipswich, MA, USA). pHAGE-dCas9-mCherry-CRY2 was generated by replacing 2XmCherry in pHAGE-dCas9-3XmCh with PCR-amplified CRY2hiclu using NotI/XhoI sites. pHAGE-dCas9-3XmCherry-CRY2 and pHAGE-dCas9-3XGFP-CRY2 were generated with the NEB HiFi DNA assembly kit (New England Biolabs, Ipswich, MA, USA) by inserting PCR-amplified CRY2hiclu in XhoI-linearized pHAGE-dCas9-3XmCh and pHAGE-dCas9-3XGFP, respectively. pHAGE-dCas9-3XGFP-CIBN was generated by inserting PCR-amplified CIBN from pEF1a-dCas9-CIBN in pHAGE-dCas9-3XGFP using XhoI/Xba sites. .. All plasmid constructs generated in this work were verified by whole-plasmid sequencing and deposited in Addgene (see ).
In Silico:Article Title: A Genetic Method for Distinguishing Cryptic Pocillopora Species in French Polynesia without Sequencing
Article Snippet: .. A total of eight candidate enzymes were identified for further testing in silico : AciI (New England Biolabs (NEB) #R0551S, MA, USA), BanI (NEB #R0118S), BceAI (NEB #R0623S), BseYI (NEB #R0635S), EcoRV-HF (NEB #R3195S), HgaI (NEB #R0154S), NlaIV (NEB #R0126S), and SacI-HF (NEB #R3156S), and XhoI (NEB Cat # R0146S). ..
Plasmid Preparation:Article Title: Technical and biological sources of noise confound multiplexed enhancer AAV screening
Article Snippet: Plasmids were maxiprepped (Qiagen 12162) and verified using Azenta Sanger sequencing and Plasmidsaurus. .. Two micrograms of each enhancer plasmid resulting from the steps above was digested overnight with 1 μL XhoI (NEB R0146L) and 10x rCutsmart Buffer (NEB B6004S) diluted in water. .. Digested plasmids were cleaned by gel extraction on a 1% agarose gel and the ymoclean Gel DNA Recovery Kit (Zymo Research D4001).
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