KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| cPARP | Cell Signaling Technologies | Cat# 5625; RRID: AB_10699459 |
| pAKT(Ser473) | Cell Signaling Technologies | Cat# 9271; RRID: AB_329825 |
| AKT | Cell Signaling Technologies | Cat# 4685; RRID: AB_2225340 |
| RNA pol II CTD phospho-Ser2 | Millipore | Cat# 04–1571-I; RRID: AB_11212363 |
| RNA pol II CTD phospho-Ser5 | Millipore | Cat# 04–1572-I; RRID: AB_11213421 |
| RNA pol II CTD phospho-Ser7 | Millipore | Cat# 04–1570-I; RRID: AB_2801298 |
| RNA pol II | Cell Signaling Technologies | Cat# 2629; RRID: AB_2167468 |
| MYC | Abcam | Cat# ab32072; RRID: AB_731658 |
| CDK7 | Cell Signaling Technologies | Cat# 2916; RRID: AB_2077142 |
| MCL-1 | Santa Cruz Biotechnology | Cat# sc-819; RRID: AB_2144105 |
| Actin | Santa Cruz Biotechnology | Cat# sc-47778 HP; RRID: AB_2714189 |
| RNAPII | Diagenode | Cat# C15100055; RRID: AB_2750842 |
| H3K27ac | Abcam | Cat# ab4729; RRID: AB_2118291 |
|
Bacterial and virus strains | ||
| pCDH-EF-eFFLy-T2A-mCherry Plasmid | Addgene | Cat# 104833; RRID: Addgene_104833 |
|
Biological samples | ||
| Primary Patient Specimens (MCL) | Moffitt Cancer Center | N/A |
|
Chemicals, peptides, and recombinant proteins | ||
| (+)-JQ1 | Cayman Chemical | Item# 11187 |
| (R)-PFI-2 | Cayman Chemical | Item# 14678 |
| A-1331852 | Selleckchem | Cat# S7801 |
| A-366 | Cayman Chemical | Item# 16081 |
| ABT-199 | Selleckchem | Cat# S8048 |
| ABT-263 | Selleckchem | Cat# S1001 |
| A-196 | Cayman Chemical | Item# 18317 |
| Alisertib | Selleckchem | Cat# S1133 |
| AZD7762 | Selleckchem | Cat# S1532 |
| AZD8055 | Selleckchem | Cat# S1555 |
| BAY-598 | Cayman Chemical | Item# 18238 |
| BEZ-235 | Selleckchem | Cat# S1009 |
| BI-9564 | Cayman Chemical | Item# 17897 |
| Bendamustine | TargetMol | Cat# T0095 |
| Bortezomib | Selleckchem | Cat# S1013 |
| Carfizomib | Selleckchem | Cat# S2853 |
| CPA7 | DC Chemicals | Cat# DC12009 |
| CPD23 | Dana-Farber Cancer Institute Jun Qi Lab | N/A |
| Dinaciclib | Selleckchem | Cat# S2768 |
| Doxorubicin | Selleckchem | Car# S1208 |
| GSK343 | Cayman Chemical | Item# 14094 |
| GSK484 | Cayman Chemical | Item# 17488 |
| GSK591 | Cayman Chemical | Item# 18354 |
| GSK864 | Cayman Chemical | Item# 18762 |
| GSK-J4 | Cayman Chemical | Item# 12073 |
| GSK-LSD1 | Cayman Chemical | Item# 16439 |
| Ibrutinib | Selleckchem | Cat# S2680 |
| I-CBP112 | Cayman Chemical | Item# 14468 |
| INCB052793 | Incyte Corporation (Wilmington, DE) | N/A |
| INCB054329 | Incyte Corporation (Wilmington, DE) | N/A |
| INCB059872 | Incyte Corporation (Wilmington, DE) | N/A |
| Lenalidomide | Selleckchem | Cat# 1029 |
| Lumpib | Selleckchem | Cat# S1069 |
| MK-1775 | Selleckchem | Cat# S1525 |
| MS049 | Cayman Chemical | Item# 18348 |
| NVP2 | MedChemExpress | HY-12214A |
| OF-1 | Cayman Chemical | Item# 17124 |
| OICR-9429 | Cayman Chemical | Item# 16095 |
| Olaparib | Selleckchem | Cat# 1060 |
| PFI-3 | Cayman Chemical | Cat# 15267 |
| PFI-4 | Cayman Chemical | Item# 17663 |
| PIK-75 | Selleckchem | Cat# S1205 |
| PRT1000220–005 | Incyte Corporation (Wilmington, DE) | N/A |
| R406 | Selleckchem | Cat# S2194 |
| Ruxolitinib | Selleckchem | Cat# S1378 |
| S63845 | ApexBio | Cat# A8737 |
| SCH-772984 | Selleckchem | Cat# S7101 |
| SGC0946 | Cayman Chemical | Item# 13967 |
| SGC707 | Cayman Chemical | Item# 17017 |
| Silvestrol | MedChemExpress | HY-13251 |
| THZ1 | Dana-Farber Cancer Institute Nathanael Gray Lab | N/A |
| THZ531 | Dana-Farber Cancer Institute Nathanael Gray Lab | N/A |
| Trametinib | Selleckchem | Cat# S2673 |
| UNC0642 | Cayman Chemical | Item# 14604 |
| UNC1215 | Cayman Chemical | Item# 13968 |
| UNC1999 | Cayman Chemical | Item# 14621 |
| VE-821 | Selleckchem | Cat# S8007 |
| Volasertib | Selleckchem | Cat# S2235 |
|
Critical commercial assays | ||
| Universal Mycoplasma Detection Kit | ATCC | Cat# 30–1012K |
| Resazurin | R&D Systems | Cat# AR002 |
| Bovine Type I Atelo-Collagen Solution | Advanced BioMatrix | Cat# 5005-B |
| Lymphoprep | STEMCELL Technologies | Cat# 07851 |
| RNeasy Plus Mini | QIAGEN | Cat# 74134 |
| TruSeq Stranded mRNA Library Prep Kit | Illumina | Cat# RS-122–2101/2 |
| 1.5 ml Bioruptor Plus TPX microtubes | Diagenode | Cat# C30010010 |
| Bioruptor | Diagenode | Cat# B01060010 |
| Dynabeads Protein G for Immunoprecipitation | ThermoFisher Scientific | Cat# 10007D |
| RNase A | Roche | Cat# 10109169001 |
| Proteinase K | Life Technologies | Cat# AM2546 |
| ThruPLEX DNA-seq Kit | TaKaRa | Cat# R400675 |
| AMPure Beads (Agencourt AMPure XP) | Beckman Coulter Life Science | Cat# A63882 |
| Pippin Prep | SAGE Sciences | Cat# PIP0001 |
| KAPA Biosystems Library Quantification Kit | KAPA Biosystems | Cat# KK4824 |
| Pierce Kinase Enrichment Kit with ATP Probe | ThermoFisher Scientific | Cat# 88310 |
| Zeba Spin Desalting Columns, 7K MWCO, 5 mL | ThermoFisher Scientific | Cat# 89892 |
| Captisol | Selleckchem | Cat# S4592 |
| D-Luciferin | GoldBio | Cat# LUCK |
|
Deposited data | ||
| RNaseq and CHIPseq | This Paper, Gene Expression Omnibus | GEO: GSE141336 |
| ABPP Proteomics | This Paper, Proteome Xchange | ProteomeXchange: PXD005734 |
|
Experimental models: cell lines | ||
| Jeko-1 | ATCC | Cat# CRL-3006; RRID: CVCL_1865 |
| Jeko-1 IR | Tao Lab | N/A |
| SP49 | University of Pennsylvannia Mariusz A. Wasik Laboratory | N/A |
| SP49 IR | Tao Lab | N/A |
| HK | Cellosaurus | Cat# CVCL_IY38; RRID: CVCL_IY38 |
| Autologous stromal cells | Tao Lab | N/A |
|
Experimental models: organisms/strains | ||
| Mouse: NOD-SCID (NOD-scid IL2Rgnull) | The Jackson Laboratory | Cat# 001303; RRID: IMSR_JAX:001303 |
|
Software and algorithms | ||
| Bamliquidator (version 1.0) | https://github.com/BradnerLab/pipeline/wiki/bamliquidator | N/A |
| ROSE2 | https://github.com/BradnerLab/pipeline/blob/master/ROSE2_main.py | Ref: Brown et al., 2014 |
| EMMA Platform Image Processing | Ref: Silva et al., 2015 | |
| ImageJ | https://imagej.nih.gov/ij/ | RRID:SCR_003070 |
| Eclipse (Mars) | https://www.eclipse.org/mars/ | N/A |
| MATLAB R2014b | https://www.mathworks.com/products/matlab.html | RRID: SCR_001622 |
| MATLAB R2016b | https://www.mathworks.com/products/matlab.html | RRID: SCR_001622 |
| GraphPad Prism 7 | https://www.graphpad.com/ | RRID: SCR_002798 |
| R (version 3.6.1) | https://cran.r-project.org/ | RRID: SCR_003005 |
| R Studio (version 1.1.456) | https://rstudio.com/ | N/A |
| Tophat2 | https://ccb.jhu.edu/software/tophat/index.shtml | RRID:SCR_013035 |
| Cuffnorm | http://cole-trapnell-lab.github.io/cufflinks/cuffnorm/index.html | N/A |
| Bowtie2 (version 2.2.1) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml | RRID: SCR_016368, Ref: Langmead and Salzberg, 2012; Langmead et al., 2019 |
| MACS (version 1.4.1) | https://github.com/macs3-project/MACS | RRID:SCR_013291 |
| MaxQuant (version 1.2.2.5) | https://www.maxquant.org/ | RRID: SCR_014485, Ref: Cox et al.,2008 |
| KEGG | https://www.genome.jp/kegg/ | RRID: SCR_012773 |
| Enrichr | https://amp.pharm.mssm.edu/Enrichr | RRID: SCR_001575, Ref: Chen et al., 2013; Kuleshov et al., 2016 |
| GSEA | http://gsea-msigdb.org/gsea/index.jsp | RRID: SCR_003199, Ref: Subramanian et al., 2005 |
| ssGSEA (version gsea2–2.2.1) | https://github.com/broadinstitute/ssGSEA2.0 | N/A |
| Cytoscape (version 3.7.1) | https://cytoscape.org/ | RRID: SCR_003032 |
| EnrichmentMap Plugin (version 3.1.0) | http://baderlab.org/Software/EnrichmentMap | RRID: SCR_016052 |
| AutoAnnotate Plugin (version 1.2) | http://apps.cytoscape.org/apps/autoannotate | N/A |