Journal: eLife

Article Title: A twin UGUA motif directs the balance between gene isoforms through CFIm and the mTORC1 signaling pathway

doi: 10.7554/eLife.85036

Figure Lengend Snippet:

Article Snippet: The following antibodies are used for western blotting: mouse monoclonal anti-beta actin (ProteinTech, 66009-1-Ig), mouse monoclonal anti-alpha tubulin (Millipore, CP06), mouse monoclonal anti-HA (clone 16B12, BioLegend, 901501), rabbit polyclonal anti-TRIM9 (ProteinTech, 10786-1-AP), rabbit monoclonal anti-S6 ribosomal protein (Cell Signaling Technology, 2217), rabbit monoclonal anti-Phospho-S6 ribosomal protein (Ser240/244) (Cell Signaling Technology, 5364), rabbit polyclonal anti-CPSF6 (Bethyl Labs, A301-356A), rabbit polyclonal anti-BRD4 (Bethyl Labs, A301-985A), and rabbit monoclonal anti-BRD4 (Abcam, ab128874).

Techniques: cDNA Synthesis, Mutagenesis, PCR Cloning, SYBR Green Assay, Sequencing, Recombinant, Generated, Software

Journal: Molecular cell

Article Title: ZFX mediates non-canonical oncogenic functions of the androgen receptor splice variant 7 (AR-V7) in castrate-resistant prostate cancer

doi: 10.1016/j.molcel.2018.08.029

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: BRD4 inhibitors used in the study are JQ1 ( Filippakopoulos et al., 2010 ) and I-BET151 (GSK1210151A; Selleck chemical LLC).

Techniques: Immunoprecipitation, Virus, Recombinant, Electron Microscopy, Transfection, Protease Inhibitor, cDNA Synthesis, SYBR Green Assay, Purification, RNA Library Preparation, Multiplex Assay, Proliferation Assay, Mutagenesis, Magnetic Beads, Western Blot, Stripping, Membrane, shRNA, Knockdown, Control, Construct, Plasmid Preparation, Software

Journal: Cell host & microbe

Article Title: Transcriptional elongation of HSV Immediate Early genes by the Super Elongation Complex drives lytic infection and reactivation from latency

doi: 10.1016/j.chom.2017.03.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CAS: 146426-40-6; Cat# sc-202157 i-CDK9 (N2’-(trans-4-aminocyclohexyl)-5’-chloro-N6-(3-fluorobenzyl)-2,4’-bipyridine-2’,6-diamine) MedChem Express CAS: 1263369-28-3; Cat# HY-16462 Acyclovir Sigma-Aldrich CAS: 59277-89-3; Cat# A4669 Vehicle (DMSO; Dimethyl sulfoxide) Sigma-Aldrich CAS: 67-68-5; Cat# D2650 Critical Commercial Assays ISOLATE II RNA Mini Kit Bioline Cat# BIO-52073 Maxima first-strand cDNA synthesis kit ThermoFisher Scientific Cat# K1671 Quanta qScript microRNA cDNA Synthesis Kit Quanta Biosciences Cat# 95107 Dynabeads™ Antibody Coupling Kit ThermoFisher Scientific Cat# 14311D Sequence-Based Reagents siGENOME siRNA SMARTpool targeting BRD2 GE Dharmacon M-004935-02 siGENOME siRNA SMARTpool targeting BRD3 GE Dharmacon M-004936-01 siGENOME siRNA SMARTpool targeting AFF1 GE Dharmacon M-020074-02 siGENOME Individual siRNA targeting AFF4: AFF4-1 GE Dharmacon M-020276-02-0001 siGENOME Individual siRNA targeting AFF4: AFF4-2 GE Dharmacon M-020276-02-0004 FlexiTube Individual siRNA targeting BRD4: BRD4-1 Qiagen SI03190845 FlexiTube Individual siRNA targeting BRD4: BRD4-2 Qiagen SI04307009 Non-targeting siControl GE Dharmacon D-001206-13, D-001206-14 Experimental Models: Cell Lines MRC5; Normal human lung fibroblast ATCC CCL-171 HFF; Human Foreskin Fibroblast (TERT-immortalized) Gift of T. Shenk, Princeton University HEK-293; Human Embryonic Kidney ATCC CRL-1573 Vero ATCC CCL-81 Experimental Models: Organisms/Strains BALB/c mice, Female, 6–8 weeks old Taconic BALB/cAnNTac Oligonucleotides Primers used in this study are listed in Table S2 Software and Algorithms Imaris (v8.2.0) BITPLANE SEQUEST (v1.2)/Proteome Discoverer (v1.3) ThermoFisher Scaffold (v4.2.1) Proteome Software Inc.; http://www.proteomesoftware.com/products/scaffold/ SAINTexpress http://www.crapome.org ReactomeFIViz/Cytoscape (v3.4.0) http://www.cytoscape.org/ GeneTools image analysis software/G:BOX Chemi XT4 Syngene; http://www.syngene.com/ Other TriPure Isolation reagent Roche/Sigma-Aldrich Cat# 11667157001 Lysing Matrix D Tubes MP-Biomedicals Cat# 6913 Open in a separate window KEY RESOURCES TABLE The coactivator HCF-1 is critical for HSV Immediate Early (IE) gene transcription HCF-1 is associated with a network of both initiation and elongation complexes The SEC containing AFF4-P-TEFb drives HSV IE transcriptional elongation BET inhibitors increase available P-TEFb and induce HSV reactivation from latency

Techniques: Virus, Recombinant, Sequencing, Software, Isolation

Journal: Cell Genomics

Article Title: Recurrent breakpoints in the BRD4 locus reduce toxicity associated with gene amplification

doi: 10.1016/j.xgen.2025.100815

Figure Lengend Snippet:

Article Snippet: After blocking with 5% dry milk in TBS-T for 30 min, the membrane was incubated at 4°C overnight with primary antibodies against rabbit BRD4 (cat. no. 702448, ThermoFisher Scientific), rabbit BRD4-L (cat. no. A301-985A100, Bethyl Laboratories), mouse SpCas9 (cat. no. 14697, Cell Signaling Technology), or rabbit GAPDH (cat. No. 2118, Cell Signaling Technology).

Techniques: Virus, Expressing, Recombinant, Plasmid Preparation, Transfection, cDNA Synthesis, Bicinchoninic Acid Protein Assay, Software, CRISPR, Amplification, Sequencing

Journal: Cell host & microbe

Article Title: Transcriptional elongation of HSV Immediate Early genes by the Super Elongation Complex drives lytic infection and reactivation from latency

doi: 10.1016/j.chom.2017.03.007

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: CAS: 146426-40-6; Cat# sc-202157 i-CDK9 (N2’-(trans-4-aminocyclohexyl)-5’-chloro-N6-(3-fluorobenzyl)-2,4’-bipyridine-2’,6-diamine) MedChem Express CAS: 1263369-28-3; Cat# HY-16462 Acyclovir Sigma-Aldrich CAS: 59277-89-3; Cat# A4669 Vehicle (DMSO; Dimethyl sulfoxide) Sigma-Aldrich CAS: 67-68-5; Cat# D2650 Critical Commercial Assays ISOLATE II RNA Mini Kit Bioline Cat# BIO-52073 Maxima first-strand cDNA synthesis kit ThermoFisher Scientific Cat# K1671 Quanta qScript microRNA cDNA Synthesis Kit Quanta Biosciences Cat# 95107 Dynabeads™ Antibody Coupling Kit ThermoFisher Scientific Cat# 14311D Sequence-Based Reagents siGENOME siRNA SMARTpool targeting BRD2 GE Dharmacon M-004935-02 siGENOME siRNA SMARTpool targeting BRD3 GE Dharmacon M-004936-01 siGENOME siRNA SMARTpool targeting AFF1 GE Dharmacon M-020074-02 siGENOME Individual siRNA targeting AFF4: AFF4-1 GE Dharmacon M-020276-02-0001 siGENOME Individual siRNA targeting AFF4: AFF4-2 GE Dharmacon M-020276-02-0004 FlexiTube Individual siRNA targeting BRD4: BRD4-1 Qiagen SI03190845 FlexiTube Individual siRNA targeting BRD4: BRD4-2 Qiagen SI04307009 Non-targeting siControl GE Dharmacon D-001206-13, D-001206-14 Experimental Models: Cell Lines MRC5; Normal human lung fibroblast ATCC CCL-171 HFF; Human Foreskin Fibroblast (TERT-immortalized) Gift of T. Shenk, Princeton University HEK-293; Human Embryonic Kidney ATCC CRL-1573 Vero ATCC CCL-81 Experimental Models: Organisms/Strains BALB/c mice, Female, 6–8 weeks old Taconic BALB/cAnNTac Oligonucleotides Primers used in this study are listed in Table S2 Software and Algorithms Imaris (v8.2.0) BITPLANE SEQUEST (v1.2)/Proteome Discoverer (v1.3) ThermoFisher Scaffold (v4.2.1) Proteome Software Inc.; http://www.proteomesoftware.com/products/scaffold/ SAINTexpress http://www.crapome.org ReactomeFIViz/Cytoscape (v3.4.0) http://www.cytoscape.org/ GeneTools image analysis software/G:BOX Chemi XT4 Syngene; http://www.syngene.com/ Other TriPure Isolation reagent Roche/Sigma-Aldrich Cat# 11667157001 Lysing Matrix D Tubes MP-Biomedicals Cat# 6913 Open in a separate window KEY RESOURCES TABLE The coactivator HCF-1 is critical for HSV Immediate Early (IE) gene transcription HCF-1 is associated with a network of both initiation and elongation complexes The SEC containing AFF4-P-TEFb drives HSV IE transcriptional elongation BET inhibitors increase available P-TEFb and induce HSV reactivation from latency

Techniques: Recombinant, Sequencing, Software, Isolation

Journal: Molecular cell

Article Title: ZFX mediates non-canonical oncogenic functions of the androgen receptor splice variant 7 (AR-V7) in castrate-resistant prostate cancer

doi: 10.1016/j.molcel.2018.08.029

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies anti-full-length AR (AR-FL) C-terminus (C19) Santa Cruz Biotechnology catalog # sc-815X anti-AR-V7 C-terminus specific Precision Antibody AG10008 anti-pan-AR N-terminus (N20) Santa Cruz Biotechnology sc-816 anti-BRD4 ChIP Grade Bethyl A301–985A100 Mouse anti-Flag tag (M2) Sigma F1804 Mouse Anti-HA tag antibody - ChIP Grade Abcam ab9110 Anti-HA HA.11 (16B12) Covance MMS-101 P-200 anti-ZFX Thermo Fisher PA5–34376 anti-ZFX Chen et al., 2008 NA Mouse anti-ZFX Cell Signaling mAb #5419 anti-Tubulin (DM1A) Mouse mAb Cell signaling tech.

Techniques: Immunoprecipitation, Virus, Recombinant, Electron Microscopy, Transfection, Protease Inhibitor, cDNA Synthesis, SYBR Green Assay, Purification, RNA Library Preparation, Multiplex Assay, Proliferation Assay, Mutagenesis, Magnetic Beads, Western Blot, Stripping, Membrane, shRNA, Knockdown, Control, Construct, Plasmid Preparation, Software