REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Acetyl-Histone H3 (Lys27) Rabbit mAb D5E4	Cell Signaling	Cat # 8173; RRID:AB_10949503
HA-Tag Rabbit mAb C29F4	Cell Signaling	Cat # 3724; RRID:AB_1549585
Anti-BRD4 Rabbit mAb 128874	abcam	Cat # EPR5150(2); RRID:AB_2868517
Brachyury Rabbit mAb D2Z3J	Cell Signaling	Cat # 81694; RRID:AB_2799983
Anti-GFP Mouse mAb 1218	abcam	Cat # 9F9.F9; RRID:AB_298911
c-Myc Rabbit Antibody	Cell Signaling	Cat # 9402; RRID:AB_2151827
PARP Rabbit Antibody	Cell Signaling	Cat # 9542; RRID:AB_2160739
Mcl-1 Rabbit mAb D2W9E	Cell Signaling	Cat # 94296; RRID:AB_2722740
GAPDH Mouse mAb D4C6R	Cell Signaling	Cat # 97166; RRID:AB_2756824
Chemicals, peptides, and recombinant proteins
X-Gal	Sigma	Cat # 3117073001
4-Thiouridine	Sigma	Cat # T4509
Iodoacetamide	Sigma	Cat # I1149
Critical commercial assays
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	Cat # G7570
Caspase-Glo® 3/7 Assay System	Promega	Cat # G8090
NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®	NEB	Cat # E7760
NEBNext® Library Quant Kit for Illumina®	NEB	Cat # E7630
Magnetic mRNA Isolation Kit	NEB	Cat # S1550
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina	Lexogen	Cat # 015.24
Fast SYBR Green Master Mix	ThermoFisher	Cat # 4385610
Deposited data
RNA-seq	This paper	GSE153972
UM-Chor1 Parental H3K27ac ChIP-seq	Sharifnia et al.10	GSE109794
ChIP-seq	This paper	GSE153971
Experimental models: cell lines
UM-Chor1	ATCC	Cat # CRL-3270
CH22	Chordoma Foundation	N/A
293T	ATCC	Cat # CRL-3216
Oligonucleotides
HDR Templates (Table S3)	Twist Bioscience	N/A
Custom synthetic sgRNA (sgRNA_T_n_term): TTTCCCGCGCTCTCGGTGCC	Synthego	N/A
Custom oligonucleotides (Table S6)	IDT	N/A
Recombinant DNA
Phage-PGK-Flag-HA-FKBP-T(G177D)-DEST	This paper	N/A
pLV hUbC-dCas9-KRAB-T2a-Puro	Addgene	Cat # 71236
Lenti-Cas9-Blast	Addgene	Cat # 52962
pLKO5.sgRAN.EGS.tRFP	Addgene	Cat # 57823
Phage-PGK-Flag-HA-FKBP-T(WT)-DEST	This paper	N/A
Software and algorithms
Graphpad Prism 8.0	Graphpad Software	https://www.graphpad.com:443/
Fiji image processing package	Schindelin et al.69	https://fiji.sc/
Genialis Data Analysis Software	Genialis	https://www.genialis.com
ROSE2	Brown et al.70	https://bitbucket.org/young_computation/rose
mSigDB	Liberzon et al.71; Subramanian et al.72	https://www.gsea-msigdb.org/gsea/msigdb/index.jsp
Core regulatory circuitry mapper	Lin et al.36	https://github.com/linlabcode/CRC
SlamDunk	Neumann et al., 201973	https://t-neumann.github.io/slamdunk/index.html
HiSat2	Kim et al., 201574	https://ccb.jhu.edu/software/hisat2/index.shtml
Cufflinks	Trapnell et al., 201275	http://cole-trapnell-lab.github.io/cufflinks/
BWA ALN	Li and Durbin, 200976	http://bio-bwa.sourceforge.net/
MACS2	Zhang et al., 200877	https://github.com/macs3-project/MACS
Other
T RNA FISH probe	Stellaris	N/A
GAPDH RNA FISH Probe	Stellaris	N/A
T DNA FISH Probe	Empire Genomics	RP11-5E5
MCL1 DNA FISH Probe	Empire Genomics	RP11-663F24