Recombinant:Article Title: H2BK120ub and its reader RNF169 sequentially regulate replication fork remodeling and stability.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 U2OS cells (H. sapiens) ATCC HTB-96 Recombinant DNA pcDNA3.1 Thermo Fisher Scientific V79020 pcDNA3.1 FLAG-H2B WT This manuscript N/A pcDNA3.1 FLAG-H2B K120R This manuscript N/A pcDNA3.1 FLAG-H2A Pinato et al, 2009 N/A pcDNA3.1 MYC-RNF169 This manuscript N/A pcDNA3.1 RNF168 Gatti et al, 2012 N/A pOG44 Thermo Fisher Scientific V600520 pcDNA5 FRT/TO Thermo Fisher Scientific V652020 pcDNA5 FRT/TO RNF169 WT This manuscript N/A pMAL6-c6T New England Biolabs N0378S pMAL6 WT (RNF169 662–708) Panier et al, 2012 N/A pMAL6 MIU* (RNF169 662–708; A673G) This manuscript N/A pMAL6 LR* (RNF169 662–708; L699A; R700A) This manuscript N/A Antibodies Mouse anti-Actin Sigma-Aldrich RRID:AB_476744 Mouse anti-Biotin Jackson ImmunoResearch RRID:AB_2339006 Rabbit anti-Biotin Cell Signaling 39681 Mouse anti-BRCA2 Millipore RRID:AB_2067762 Rabbit anti-FLAG Sigma-Aldrich RRID:AB_439687 Mouse anti-FLAG M2 Sigma-Aldrich RRID:AB_259529 Mouse anti-c-Myc (9E10) Santa Cruz Biotechnology RRID:AB_627268 Mouse anti-GAPDH Merck RRID:AB_2107445 Rabbit anti-Histone H2A Millipore RRID:AB_11212920 Rabbit anti-Histone H3 Abcam RRID:AB_302613 Rabbit anti-Histone H2B Abcam RRID:AB_302612 Rabbit anti-H2BK120ub Cell Signaling 5546S Mouse anti-H3K9me3 Abcam ab317790 Rabbit anti-Lamin A Sigma-Aldrich RRID:AB_532254 Rabbit anti-MCM7 Cell Signaling RRID:AB_2142705 Rabbit anti-pCHK1 (S345) Cell Signaling 2348S Mouse anti-CHK1 Santa Cruz Biotechnology RRID:AB_627257 Rabbit anti-pRPA32 (S4/S8) Bethyl RRID:AB_210547 Mouse anti-RPA Millipore RRID:AB_11205561 Mouse anti-TFIIH Boster Biol. .. Reagent/resource Reference or source Identifier or catalog number Flp-In T-REx Core Kit Thermo Fisher Scientific K650001 Software Olympus ScanR image analysis software (version 3.0.1) Olympus Life Science www.olympuslifescience.com Spotfire data visualization software (version 7.0.1) TIBCO Software Inc. www.spotfire.com GraphPad Prism 10 for MAC OS GraphPad Software www.graphpad.com FlowJo 10.6.1 FlowJo Software www.flowjo.com
Article Title: HSC70 coordinates COP9 signalosome and SCF ubiquitin ligase activity to enable a prompt stress response.
Article Snippet: The SCF (SKP1/CUL1/F-box protein) ubiquitin ligase complex plays a protective role against external stress, such as ultraviolet irradiation.. The emergence of substrates activates SCF through neddylation, the covalent attachment of ubiquitin-like protein NEDD8 to CUL1.. After substrate degradation, SCF is inactivated through deneddylation by COP9-signalosome (CSN), a solo enzyme that can deneddylate SCF.
Article Title: Speedy A governs non-homologous XY chromosome desynapsis as a unique prerequisite for XY loop-axis organization.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 C57BL6/J (M. musculus) CYAGEN N/A Recombinant DNA pcDNA3.1(+) ThermoFisher V79020 pcDNA3.1-SpdyaWT-HA This study N/A pcDNA3.1-SpdyaA125V-HA This study N/A pcDNA3.1-Cdk2-Myc This study N/A pcDNA3.1-Sun1WT-FLAG This study N/A 16 The EMBO Journal © The Author(s) D ow nloaded from https://w w w .em bopress.org on A ugust 22, 2025 from IP 103.21.124.79. .. All mouse lines used in this study were generated in the C57BL/6J genetic background by Cyagen Biosciences (Suzhou, China) using the CRISPR/Cas9-mediated genome-editing system unless otherwise specified.
Article Title: Maintenance of p-eIF2α levels by the eIF2B complex is vital for colorectal cancer.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 SW480 cells (H. sapiens) ATCC CCL-228 DLD1 cells (H. sapiens) ATCC CCL-221 Reagent/resource Reference or source Identifier or catalog number PaTu8988 cells (H. sapiens) Mathias Rosenfeldt, EKO, Oberhausen N/A HEK293-Noggin (H. sapiens) Elmar Wolf, CAU Kiel N/A L17-R-spondin (H. sapiens) Owen J. Sansom, CRUK Scotland Institute, Glasgow WT organoids (M. musculus) This study N/A A organoids (M. musculus) Owen J. Sansom, CRUK Scotland Institute, Glasgow (el Marjou et al, 2004; Sansom et al, 2007; Shibata et al, 1997) N/A AK organoids (M. musculus) Owen J. Sansom, CRUK Scotland Institute, Glasgow (el Marjou et al, 2004; Sansom et al, 2007; Shibata et al, 1997) N/A LAKTP organoids (M. musculus) Eduard Batlle, IRB, Barcelona (Tauriello et al, 2018) N/A T4 organoids (H. sapiens) Schmidt et al, 2019 N/A FAP organoids (H. sapiens) This study N/A HD-3 organoids (H. sapiens) Rene-Filip Jackstadt, HiStem Heidelberg N/A Ko165 organoids (H. sapiens) This study, Nicolas Schlegel, University Hospital Würzburg N/A Recombinant DNA psPAX2 Didier Trono, Addgene #12260 pMD2.G Didier Trono, Addgene #12259 pLeGO Hygro shEIF2B1-3 This study N/A pLeGO Hygro shEIF2B2-1 This study N/A pLeGO Hygro shEIF2B3-5 This study N/A pLeGO Hygro shEIF2B4-2 This study N/A pLeGO Hygro shEIF2B5-3 Schmidt et al, 2019 N/A pLeGO Hygro shLuciferase (shCTRL) Schmidt et al, 2019 N/A LT3-GEPIR-shEIF2B1-1 This study N/A LT3-GEPIR-shEIF2B1-2 This study N/A LT3-GEPIR-shEif2b1-1 This study N/A LT3-GEPIR-shEif2b1-2 This study N/A LT3-GEPIR-shEif2b4 This study N/A LT3-GEPIR-shEIF2B4 This study N/A LT3-GEPIR-shCTRL This study N/A pRRL-SFFV-puro-eIF2Bαwt This study N/A pRRL-SFFV-puro-eIF2Bαmut This study N/A pRRL-SFFV-puro-eIF2Bδwt This study N/A pRRL-SFFV-puro-eIF2Bδmut This study N/A pRRL-SFFV-puro-6xHis-HAeIF2Bαwt This study N/A pRRL-SFFV-puro-6xHis-HAeIF2Bαmut This study N/A pRRL-SFFV-puro-HA-eIF2Bδwt This study N/A pRRL-SFFV-puro-HA-eIF2Bδmut This study N/A pRRL-SFFV-puro-HA-eIF2αwt This study N/A pRRL-SFFV-puro-HA-eIF2αS51A This study N/A pRRL-SFFV-puro-HA-eIF2αS51D This study N/A pLV-Bsd-EIF2Bεwt-HA Schmidt et al, 2019 N/A pLV-Bsd-EIF2BεR113H-HA This study N/A © The Author(s) The EMBO Journal 15 D ow nloaded from https://w w w .em bopress.org on M arch 1, 2025 from IP 2401:4900:1ce1:f8ae:54ac:d0c0:de67:d2a. .. Reagent/resource Reference or source Identifier or catalog number IntestiCultTM Organoid Growth Medium (Human) Stemcell Technologies 6010 DMEM Capricorn Scientific DMEM-HPA RPMI 1640 Thermo Fisher Scientific 21875091 FBS Capricorn Scientific FBS-11A doxycycline Sigma D9891 cycloheximide Sigma C7698 tunicamycin Sigma T7765 ISRIB Sigma SML0843 RNaseI Ambion (Invitrogen) AM2295 (lot# 00791236) SUPERaseInTM Ambion (Invitrogen)csx AM2696 NEXTflex small RNA kit (v3 - discontinued) Perkin Elmer (now Revvity) NOVA-513205 CORALL total RNA seq kit (v1 - discontinued) Lexogen 095.96 RiboCop (H/M/R) (v2) Lexogen 144.96 NextSeq 500/550 High Output Kit v2.5 (75 Cycles) Illumina 20024906 Software ImageJ v1.53t https://imagej.net/ij/ GraphPad Prism v10.0.3 for Mac https://www.graphpad.com/ scientific-software/prism/ Harmony High Content Imaging and Analysis Software v4.8 http://www.perkinelmer.de/ product/harmony-4-8-officehh17000001 StepOne software v2.3 https:// www.thermofisher.com/de/ de/home/technicalresources/softwaredownloads/StepOne-andStepOnePlus-Real-Time-PCRSystem.html Multi Gauge software v3.0 https:// cloudfront.ualberta.ca/-/ media/science/departments/ biological-sciences/mbsu/fla5000/mulitgauge20.pdf BD FACSDIVA Software v9.0.1 http:// www.bdbiosciences.com/us/ instruments/research/ software/flow-cytometryacquisition/bd-facsdivasoftware/m/111112/overview TecanSpark Control v3.1 Tecan Trading AG IncuCyte 2021C Sartorius Fusion FX Evolution Capt Edge v18.14.0.0 Vilber Microsoft Office version 16.16.27 University Wuerzburg Affinity Designer version 2.2.1 https://affinity.serif.com/de/ Molecular Operating Environment 2019.01 ULC CCG (2019) Chemical Computing Group ULC, 1010 Sherbrooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2019 ZEN software Zeiss R v 4.3.2 (2023-10-31) RStudio v 2023.12.0, Build 369 Other Fusion FX Vilber Image Reader LAS 4000 Fujifilm Reagent/resource Reference or source Identifier or catalog number TecanSpark Tecan Incucyte SX5 Sartorius StepOne Plus Real-Time PCR System Applied Biosystems NextSeq 500 sequencer Illumina OperettaTM High-Content Screening System Perkin Elmer (now Revvity) BD FACS CantoTM II BD Biosciences
Sequencing:Article Title: HSC70 coordinates COP9 signalosome and SCF ubiquitin ligase activity to enable a prompt stress response.
Article Snippet: The SCF (SKP1/CUL1/F-box protein) ubiquitin ligase complex plays a protective role against external stress, such as ultraviolet irradiation.. The emergence of substrates activates SCF through neddylation, the covalent attachment of ubiquitin-like protein NEDD8 to CUL1.. After substrate degradation, SCF is inactivated through deneddylation by COP9-signalosome (CSN), a solo enzyme that can deneddylate SCF.
Ubiquitin Proteomics:Article Title: HSC70 coordinates COP9 signalosome and SCF ubiquitin ligase activity to enable a prompt stress response.
Article Snippet: The SCF (SKP1/CUL1/F-box protein) ubiquitin ligase complex plays a protective role against external stress, such as ultraviolet irradiation.. The emergence of substrates activates SCF through neddylation, the covalent attachment of ubiquitin-like protein NEDD8 to CUL1.. After substrate degradation, SCF is inactivated through deneddylation by COP9-signalosome (CSN), a solo enzyme that can deneddylate SCF.
Software:Article Title: HSC70 coordinates COP9 signalosome and SCF ubiquitin ligase activity to enable a prompt stress response.
Article Snippet: The SCF (SKP1/CUL1/F-box protein) ubiquitin ligase complex plays a protective role against external stress, such as ultraviolet irradiation.. The emergence of substrates activates SCF through neddylation, the covalent attachment of ubiquitin-like protein NEDD8 to CUL1.. After substrate degradation, SCF is inactivated through deneddylation by COP9-signalosome (CSN), a solo enzyme that can deneddylate SCF.
Western Blot:Article Title: Neuralized-like proteins differentially activate Notch ligands.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 U2OS cells (H. sapiens) ATCC HTB-96 Drosophila melanogaster starins (D. mel.): mib1EY09870 Lai EC, 2005 ptc-GAL4 Speicher SA, 1994 DlattP Viswanathan R, 2019 DlattP-Dl-NEQN2A-HA Troost T, 2023 Antibodies Anti-Flag for IP Sigma-Aldrich F1804 Anti-Flag for WB BioLegend 902401 Anti-HA for WB Covance PRB-101C anti-Wg for IF DSHB 4D4 anti-HA for IF Cell Signalling C29F4 anti-V5 for IF Invitrogen #R960-25 anti-myc for IF Cell Signalling 9B11 anti-rabbit Alexa568 for IF Invitrogen A-21235 anti-mouse Alexa647 for IF Invitrogen A-11011 Chemicals, enzymes and other reagents Lipofectamine 3000 Thermo Fisher L3000008 TransIT-X2 Mirus MIR 6000 DMEM, high glucose with L-glutamine Sartorius 01-052-1 A Penicillin streptomycin Biowest L0022-100 Fetal bovine serum (FBS) Biowest S1400-500 Protease inhibitor cocktail Calbiochem 539131 Anti-mouse IgG-agarose beads Sigma-Aldrich, Merck A-6531 PFA Electron Microscopy Sciences 19200 Triton X-100 Sigma-Aldrich, Merck 1003267647 Normal goat serum (NGS) Biozol Diagnostica Vertrieb GmbH ENG9010-10 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on N ovem ber 8, 2025 from IP 2400:1a00:4ba5:c093:f5ff:4dcd:7589:c171. .. Reagent/resource Reference or source Identifier or catalogue number Vectashield Vector laboratories H-1000 Passive lysis buffer Promega E1941 Wizard(R) Plus SV Minipreps DNA Purif.
Protease Inhibitor:Article Title: Neuralized-like proteins differentially activate Notch ligands.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 U2OS cells (H. sapiens) ATCC HTB-96 Drosophila melanogaster starins (D. mel.): mib1EY09870 Lai EC, 2005 ptc-GAL4 Speicher SA, 1994 DlattP Viswanathan R, 2019 DlattP-Dl-NEQN2A-HA Troost T, 2023 Antibodies Anti-Flag for IP Sigma-Aldrich F1804 Anti-Flag for WB BioLegend 902401 Anti-HA for WB Covance PRB-101C anti-Wg for IF DSHB 4D4 anti-HA for IF Cell Signalling C29F4 anti-V5 for IF Invitrogen #R960-25 anti-myc for IF Cell Signalling 9B11 anti-rabbit Alexa568 for IF Invitrogen A-21235 anti-mouse Alexa647 for IF Invitrogen A-11011 Chemicals, enzymes and other reagents Lipofectamine 3000 Thermo Fisher L3000008 TransIT-X2 Mirus MIR 6000 DMEM, high glucose with L-glutamine Sartorius 01-052-1 A Penicillin streptomycin Biowest L0022-100 Fetal bovine serum (FBS) Biowest S1400-500 Protease inhibitor cocktail Calbiochem 539131 Anti-mouse IgG-agarose beads Sigma-Aldrich, Merck A-6531 PFA Electron Microscopy Sciences 19200 Triton X-100 Sigma-Aldrich, Merck 1003267647 Normal goat serum (NGS) Biozol Diagnostica Vertrieb GmbH ENG9010-10 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on N ovem ber 8, 2025 from IP 2400:1a00:4ba5:c093:f5ff:4dcd:7589:c171. .. Reagent/resource Reference or source Identifier or catalogue number Vectashield Vector laboratories H-1000 Passive lysis buffer Promega E1941 Wizard(R) Plus SV Minipreps DNA Purif.
Electron Microscopy:Article Title: Neuralized-like proteins differentially activate Notch ligands.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 U2OS cells (H. sapiens) ATCC HTB-96 Drosophila melanogaster starins (D. mel.): mib1EY09870 Lai EC, 2005 ptc-GAL4 Speicher SA, 1994 DlattP Viswanathan R, 2019 DlattP-Dl-NEQN2A-HA Troost T, 2023 Antibodies Anti-Flag for IP Sigma-Aldrich F1804 Anti-Flag for WB BioLegend 902401 Anti-HA for WB Covance PRB-101C anti-Wg for IF DSHB 4D4 anti-HA for IF Cell Signalling C29F4 anti-V5 for IF Invitrogen #R960-25 anti-myc for IF Cell Signalling 9B11 anti-rabbit Alexa568 for IF Invitrogen A-21235 anti-mouse Alexa647 for IF Invitrogen A-11011 Chemicals, enzymes and other reagents Lipofectamine 3000 Thermo Fisher L3000008 TransIT-X2 Mirus MIR 6000 DMEM, high glucose with L-glutamine Sartorius 01-052-1 A Penicillin streptomycin Biowest L0022-100 Fetal bovine serum (FBS) Biowest S1400-500 Protease inhibitor cocktail Calbiochem 539131 Anti-mouse IgG-agarose beads Sigma-Aldrich, Merck A-6531 PFA Electron Microscopy Sciences 19200 Triton X-100 Sigma-Aldrich, Merck 1003267647 Normal goat serum (NGS) Biozol Diagnostica Vertrieb GmbH ENG9010-10 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on N ovem ber 8, 2025 from IP 2400:1a00:4ba5:c093:f5ff:4dcd:7589:c171. .. Reagent/resource Reference or source Identifier or catalogue number Vectashield Vector laboratories H-1000 Passive lysis buffer Promega E1941 Wizard(R) Plus SV Minipreps DNA Purif.
Next-Generation Sequencing:Article Title: Neuralized-like proteins differentially activate Notch ligands.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalogue number Experimental models HEK293T cells (H. sapiens) ATCC CRL-3216 U2OS cells (H. sapiens) ATCC HTB-96 Drosophila melanogaster starins (D. mel.): mib1EY09870 Lai EC, 2005 ptc-GAL4 Speicher SA, 1994 DlattP Viswanathan R, 2019 DlattP-Dl-NEQN2A-HA Troost T, 2023 Antibodies Anti-Flag for IP Sigma-Aldrich F1804 Anti-Flag for WB BioLegend 902401 Anti-HA for WB Covance PRB-101C anti-Wg for IF DSHB 4D4 anti-HA for IF Cell Signalling C29F4 anti-V5 for IF Invitrogen #R960-25 anti-myc for IF Cell Signalling 9B11 anti-rabbit Alexa568 for IF Invitrogen A-21235 anti-mouse Alexa647 for IF Invitrogen A-11011 Chemicals, enzymes and other reagents Lipofectamine 3000 Thermo Fisher L3000008 TransIT-X2 Mirus MIR 6000 DMEM, high glucose with L-glutamine Sartorius 01-052-1 A Penicillin streptomycin Biowest L0022-100 Fetal bovine serum (FBS) Biowest S1400-500 Protease inhibitor cocktail Calbiochem 539131 Anti-mouse IgG-agarose beads Sigma-Aldrich, Merck A-6531 PFA Electron Microscopy Sciences 19200 Triton X-100 Sigma-Aldrich, Merck 1003267647 Normal goat serum (NGS) Biozol Diagnostica Vertrieb GmbH ENG9010-10 © The Author(s) EMBO reports 13 D ow nloaded from https://w w w .em bopress.org on N ovem ber 8, 2025 from IP 2400:1a00:4ba5:c093:f5ff:4dcd:7589:c171. .. Reagent/resource Reference or source Identifier or catalogue number Vectashield Vector laboratories H-1000 Passive lysis buffer Promega E1941 Wizard(R) Plus SV Minipreps DNA Purif.
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