Nature - USA (2020-02-13)

3

nature research | reporting summary

April 2018

Eukaryotic cell lines

Policy information about cell lines

Cell line source(s) The source and authentication of all eukaryotic cells in the study is presented in SI Table.

Authentication Cell lines were authenticated using GenePrint 10 STR Authentication Kit (Promega, Madison, WI)

Mycoplasma contamination Cell lines were tested for mycoplasma using MycoAlert Detection Kit (Lonza,

Walkersville, MD) and all lines tested negative.

Commonly misidentified lines

(See ICLAC register)

No commonly misidentified lines used in this study

Animals and other organisms

Policy information about studies involving animals; ARRIVE guidelines recommended for reporting animal research

Laboratory animals NSG-male mice (Jackson Laboratory), Fox Chase SCID® (Charles River Labs) mice, and Sprague Dawley (Crl:CD(SD)) rat strain from

commercial sources were used. Male rat 56-58 days of age at initiation of testing article administration were used. NSG and Fox

Chase SCID® male mice 6-8 weeks of age at time of study initiation were used.

Wild animals No wild animals used in the study

Field-collected samples No field-collected samples used in the study

ChIP-seq

Data deposition

Confirm that both raw and final processed data have been deposited in a public database such as GEO.

Confirm that you have deposited or provided access to graph files (e.g. BED files) for the called peaks.

Data access links

May remain private before publication.

Accession GSE118152, GSE118247

Files in database submission Provide^ a^ list^ of^ all^ files^ available^ in^ the^ database^ submission.

Genome browser session

(e.g. UCSC)

Provide a link to an anonymized genome browser session for "Initial submission" and "Revised version" documents only, to

enable peer review. Write "no longer applicable" for "Final submission" documents.

Methodology

Replicates Each ChIP-Seq experiment was n=1.

Sequencing depth All experiments were single end, 75 nt reads. For individual experiments total/usable: BRD4 DHT 39,825,247/22,844,767;

BRD4DHT ABBV-744 37,353,171/18,060657; BRD4 DHT ABBV-075 38,458,410/22,734,829; BRD4 DHT ENZ

34,719,339/21,325,188; AR 39,178,357/27,668,040; H3K27Ac 33,779,643/26,271,979.

Antibodies Active Motif H3K27Ac cat#39133 lot 8, Bethyl BRD4 cat#A301-985A lot 6, Santa Cruz AR cat#sc-13062 lotB2616.

Peak calling parameters Peaks were called using MACS2.1.0 narrow, pvalue cutoff 1e-7.

Data quality Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed.

Software Illumina Casava 1.8 software used for basecalling. Reads were aligned to hg19 using BWA algorithm, USeq platform for

Intersecting Regions and Neighboring Gene identifications (http://useq.sourceforge.net/). Further analysis of aligned bam

files was done using NGSPlot (https://github.com/shenlab-sinai/ngsplot) to visualize heatmaps and generate average profile

plots. NGSPlot provided heatmap and average profile plot figures.