KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-HDAC3 (1:500) | Abcam | Cat# ab32369 RRID: AB_732780 |
| Anti-HDAC8 (1:1,000) | Abcam | Cat# ab187139 RRID: AB_2715505 |
| Anti-HDAC6 (1:1,000) | Cell Signaling Technology | Cat# 7558 RRID: AB_10891804 |
| Anti-GAPDH (1:10,000) | Millipore-Sigma | Cat# G8795 RRID: AB_1078991 |
| Anti-Vinculin (1:1,000) | Santa Cruz | Cat# sc-73614 RRID: AB_1131294 |
| Anti-Mouse IgG (1:10,000) | LiCor | Cat# 92668072 RRID: AB_10953628 |
| Anti-Rabbit IgG (1:10,000) | LiCor | Cat# 92632211 RRID: AB_621843 |
| Chemicals, peptides, and recombinant proteins | ||
| cOmplete, Mini Protease Inhibitor Cocktail | Sigma-Aldrich | Cat# 11836153001 |
| PhosSTOP Phosphatase Inhibitor Tablets | Sigma-Aldrich | Cat# 04906837001 |
| Halt Protease and Phosphatase Inhibitor Single-Use Cocktail | Thermo Fisher Scientific | Cat# 78442 |
| dBET6 | A gift from Gray Lab, Stanford University | N/A |
| AT1 | Tocris | Cat# 6356 |
| MLN4924 | MedChemExpress | Cat# HY-70062 |
| BRD4BD2-GFP-P2a-mCherry | Fischer Lab, Dana-Farber Cancer Institute (Nowak et al., 2018) | N/A |
| HDAC8-EGFP-IRES-mCherry | Fischer Lab, Dana-Farber Cancer Institute | N/A |
| Critical commercial assays | ||
| Tandem Mass Tag (TMT) Reagents: 11plex | Thermo Fisher Scientific | Cat# A34808 |
| Tandem Mass Tag (TMT) Reagents: 16plex | Thermo Fisher Scientific | Cat# A44520 |
| Bradford Reagent | BioRad | Cat# 500-0205 |
| CellTiter Glo | Promega | Cat# G7570 |
| Histone Deacetylase in vitro inhibition assay | Reaction Biology | www.reactionbiology.com |
| Deposited data | ||
| wp-esf_110 | This paper | PXD023630 |
| wp-esf_120 | This paper | PXD023652 |
| wp-esf_126 | This paper | PXD023583 |
| wp-esf_127 | This paper | PXD026272 |
| wp-esf_130 | This paper | PXD023627 |
| wp-esf_132 | This paper | PXD026276 |
| wp-esf_155 | This paper | PXD023633 |
| wp-esf_162 | This paper | PXD023636 |
| wp-esf_178 | This paper | PXD026278 |
| wp-esf_221 | This paper | PXD026277 |
| wp-esf_229 | This paper | PXD026430 |
| wp-esf_241 | This paper | PXD026398 |
| wp-esf_242 | This paper | PXD026397 |
| Experimental models: Cell lines | ||
| MM.1S (H. sapiens) | ATCC | CRL-2974; RRID:CVCL_8792 |
| KELLY (H. sapiens) | Sigma-Aldrich | 92110411; RRID:CVCL_2092 |
| HEK293T cells (H. sapiens) | ATCC | CRL-3216; RRID:CVCL_0063 |
| Recombinant DNA | ||
| Cilantro2 | (Sievers et al., 2018) | Addgene Cat# 74450 |
| Software and algorithms | ||
| Proteome Discoverer 2.2, 2.4 | Thermo Fisher Scientific | RRID: SCR_014477 https://thermo.flexnetoperations.com/control/thmo/login |
| R Framework | Team RCR: A Language and Environment for Statistical Computing | http://www.R-project.org/ |
| Statistical Analysis Limma Package (R framework) | Ritchie et al. (2015) Nucleic Acids Res. | https://bioconductor.org/packages/release/bioc/html/limma.html |
| Prism 8 | GraphPad | RRID: SCR_002798 http://www.graphpad.com/ |