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mouse monoclonal anti-ha.11 antibody (clone 16b2)  (Covance)

 
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    Structured Review

    Covance mouse monoclonal anti-ha.11 antibody (clone 16b2)
    Mouse Monoclonal Anti Ha.11 Antibody (Clone 16b2), supplied by Covance, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/ha%2E11+antibody/anti+ha/pm40440169-174-2-12
    Average 90 stars, based on 1 article reviews
    mouse monoclonal anti-ha.11 antibody (clone 16b2) - by Bioz Stars, 2026-09
    90/100 stars

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    Blocking Assay:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Marker:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Virus:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Recombinant:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Electron Microscopy:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Western Blot:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Chromatin Immunoprecipitation:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Next-Generation Sequencing:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Immunofluorescence:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Biomarker Discovery:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Clone Assay:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).

    Binding Assay:

    Article Title: Characterization of the HHV-6B U20 Immunoevasin.
    Article Snippet: Roseoloviruses (human herpesvirus 6A [HHV-6A], -6B, and -7) infect .90% of the human population during early childhood and are thought to remain latent or persistent throughout the life of the host.. As such, these viruses are among the most pervasive and stealthy of all viruses; they must necessarily excel at escaping immune detection throughout the life of the host, and yet, very little is known about how these viruses so successfully escape host defenses.. Here, we characterize the expression, trafficking, and posttranslational modifications of the HHV6B U20 gene product, which is encoded within a block of genes unique to the roseoloviruses.

    Article Title: Exploring the Expression and Function of cTyro3, a Candidate Zika Virus Receptor, in the Embryonic Chicken Brain and Inner Ear.
    Article Snippet: The primary antibodies were diluted in blocking solution as follows: anti-GFP (1:1000, rabbit IgG, Invitrogen, Waltham, MA, USA, A11122), HA.11 (1:500, mouse IgG1, Covance, Princeton, NJ, USA, MMS-101P), dsRNA (1:500, J2, mouse IgG2a, SCICONS), 3C2 (1:5–1:40, mouse IgG1 hybridoma culture supernatant) [63], anti-HCS-1 (1:100, mouse IgG, BD Biosciences, San Jose, CA, USA), and axonal marker 3A10 (1:50, mouse IgG1, DSHB #3A10, AB_531874).

    Article Title: Mitochondrial cristae-remodeling protein OPA1 in POMC neurons couples Ca 2+ homeostasis with adipose tissue lipolysis
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Alpha-MSH Millipore Cat# AB5087; RRID: AB_91683 Alpha-Tubulin Sigma-Aldrich Cat# T6199; RRID: AB_477583 Alexa Fluor 594 chicken anti-mouse ThermoFisher Cat# A-21201; RRID: AB_2535787 Alexa Fluor 488 chicken anti-rabbit ThermoFisher Cat# A-21441; RRID: AB_2535859 Alexa Fluor 488 donkey anti-sheep ThermoFisher Cat# A-11015; RRID: AB_2534082 Alexa Fluor 594 donkey anti-rabbit ThermoFisher Cat# A-21207; RRID: AB_141637 Alexa Fluor 647 donkey anti-rabbit ThermoFisher Cat# A32795; RRID: AB_2762835 Anti-mouse HRP GE Healthcare UK Limited Cat# NA931; RRID: AB_772210 Anti-Rabbit HRP GE Healthcare UK Limited Cat# NA934; RRID: AB_2722659 b-Actin Sigma-Aldrich Cat# A2066; RRID: AB_476693 GFP Aves Labs Cat# GFP-1010; RRID: AB_2307313 HA.11 Covance Cat# MMS-101R; RRID: AB_291262 HSL-PSer563 Cell Signaling Cat# 4139; RRID: AB_2135495 HSL-PSer660 Cell Signaling Cat# 4126; RRID: AB_490997 HSL Cell Signaling Cat# 4107; RRID: AB_2296900 OPA1 BDBiosciences Cat# 612606; RRID: AB_399888 OPA1 Novus Biologicals Cat# NB110-55290C; RRID: AB_1851209 OXPHOS Rodent Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 Perilipin Cell Signaling Cat# 3467; RRID: AB_2167270 POMC Phoenix Pharmaceuticals Cat# H-029-30; RRID: AB_2307442 TOM20 Santa Cruz Cat# sc-11415; RRID: AB_2207533 Bacterial and virus strains AAV8-hSYN-DIO-hM3D(Gq)-mCherry Addgene Cat# 44361 AAV8-hSYN-DIO-hM4D(Gi)-mCherry Addgene Cat# 44362 pGP-Syn-FLEX-jGCaMP7s-WPRE Addgene Cat# 10449-AAV9 pAAV-FLEX-EF1A-mtGCaMP6s-WPRE Vector builder This paper pAAV-FLEX-tdTomato Addgene Cat# 28306-AAV9 Chemicals, peptides, and recombinant proteins 3-3’-Diaminobenzidine Sigma-Aldrich Cat# D5637 Adenosine diphosphate (ADP) Calbiochem Cat# 117105 Alpha-MSH Sigma-Aldrich Cat# M4135 Angiotensin II Sigma-Aldrich Cat# A9525 Antimycin A Sigma-Aldrich Cat# A8674 Artificial cerebrospinal fluid (aCSF) Tocris Bioscience Cat# 3525 Buffer RLT Qiagen Cat# 79216 Carbonyl cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP) Sigma-Aldrich Cat# C2920 Clozapine-N-oxide Tocris Cat# C4936 Dental acrylic TAB2000 , liquid Kerr Cat#61775 Dental acrylic TAB2000 , powder Kerr Cat#61771 Digitonin Sigma-Aldrich Cat# D5628 Durcupan Electron Microscopy Sciences Cat# 14040 Dynabeads Protein G ThermoFisher Cat# 10004D Enhanced chemiluminescence reagent Pierce Cat# 32105 (Continued on next page) e1 Cell Metabolism 33, 1820–1835.e1–e9, September 7, 2021

    Article Title: A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6
    Article Snippet: Where indicated, HA-tagged proteins were detected by the mouse monoclonal antibody HA.11 (Covance) and p53 was detected with the mouse monoclonal antibody DO-1 (CalBiochem).

    Article Title: HP1 drives de novo 3D genome reorganization in early Drosophila embryos
    Article Snippet: HP1 Developmental Studies Hybridoma Bank C1A9 (validated by western blot and ChIP in HP1-KD in ED Fig. 1g and 3b) HP1 Covance, PRB-291C-200 HA (C29F4) Cell Signaling #3724S (according to manufacturer used in 866 oublications, validated for ChIP) HA.11 Covance MMS-101P H3K9ac ActiveMotif 39586 (according to manufacturer used in 7 publications, validated for ChIP) H3K9ac ActiveMotif 39918 (according to manufacturer validated for ChIP and NGS applications) H3K9me3 ActiveMotif 39161 (according to manufacturer validated for ChIP and NGS applications) H3K9me2 ActiveMotif 39239 (validated by immunofluorescence in K9M in ED Fig. 4a) H3K9me3 Abcam ab176916 (according to manufacturer used in 11 publications, validated for ChIP) H3K27me3 Diagenode, C15410195 (Lot A1811-001P) (validated by ChIP in E(z)-KD in Zenk et al. 2017, Science) H3K4me1 Diagenode, C15410194 (Lot A1862D) (according to manufacturer used in 44 publications, validated for ChIP) H3K4me3 Diagenode, C15410003 (according to manufacturer used in 184 publications, validated for ChIP) H3K27ac Diagenode, C15410196 (Lot A1723-041D) (according to manufacturer validated for ChIP and NGS applications) Rpb3 (PolII) Carla Margulies Lab Tubulin DM1 Sigma T9026 H3 ActiveMotif MABI 0301 Rpb3 (PolII) Asifa Akhtar Lab (validated by western blot in Rpb3 KD embryos) Eukaryotic cell lines Policy information about cell lines Cell line source(s) We used S2 cell line provided by Dr. Michael Boutros, DKFZ, Heidelberg.

    Article Title: Sumoylation of SAP130 regulates its interaction with FAF1 as well as its protein stability and transcriptional repressor function.
    Article Snippet: The following antibodies were purchased: HA (HA.11; Babco/Covance, Berkley, CA), HA (Biolegend, San Diego, CA), FLAG (M2; Sigma), c-Myc (9E10; GeneTex, Taiwan), GFP (JL-8; BD Biosciences Clontech), FAF1 (C1C3; GeneTex, San Antonio, TX); SAP130 (12130–1-AP, Proteintech), HDAC1 (10E2, Cell Signaling Technology), SIN3A (D9D6, Cell Signaling Technology) and actin (clone AC-74; Sigma, St. Louis, MO).

    Article Title: LONP1 and mtHSP70 cooperate to promote mitochondrial protein folding
    Article Snippet: Cells were fixed in 10% formaldehyde, permeabilized in 0.1% Triton X-100, and immunostained with antibody against FLAG M2 (Sigma, 1:500), HA.11 (Covance, 1:500), TOM20 (Santa Cruz BioTech, 1:500) or HSP60 (Santa Cruz BioTech, 1:500).

    Article Title: Tandem Immunoaffinity Purification Using Anti-FLAG and Anti-HA Antibodies.
    Article Snippet: The immunoaffinity purification of target proteins followed by the identification and characterization of associated proteins by mass spectrometry is a widely used technique.. An immunoaffinity purification bears resemblance to a standard immunoprecipitation; however, the end product for mass spectrometric analysis in the femtomole (10) to attomole (10) range is required to be of exceptional purity.. This high degree of sensitivity in detection renders it of extreme importance to eliminate most if not all of the nonspecific background proteins and can be achieved by performing a tandem affinity purification (TAP).



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