Nature - USA (2020-01-02)

6

nature research | reporting summary

October 2018

Methodology

Replicates HEK293 Flag ChIP-seq: wt, T1 ,T2, T3 and control: 2 replicates

HEK293 Flag-ENL wt, T1, T2 and T3 RNA-seq: 2 replicates

HK-2 Flag-ENL wt, T1, T2 and T3 RNA-seq: 2 replicates

all others: 1 replicate

Note: Key target genes were validated by ChIP-qPCR and gene expression qPCR analyses for all conditions in additional,

independent repeated experiments (n>3).

Sequencing depth Sample Sequencing depth

GSM3564782 ChIPSeq.PolII_S2P_T1_mut 74852492

GSM3564783 ChIPSeq.PolII_S2P_T2_mut 86431056

GSM3564784 ChIPSeq.PolII_S2P_T3_mut 82360591

GSM3564785 ChIPSeq.PolII_S2P_WT_ENL 67652603

GSM3564786 ChIPSeq.CDK9_T1_mut 66925666

GSM3564787 ChIPSeq.CDK9_T2_mut 76629800

GSM3564788 ChIPSeq.CDK9_T3_mut 94390261

GSM3564789 ChIPSeq.CDK9_WT_ENL 84910393

GSM3564790 ChIPSeq.HEK293_WT_ENL_B 68322465

GSM3564791 ChIPSeq.HEK293_T1_mut_C 93069874

GSM3564792 ChIPSeq.HEK293_T1_Y78A_mut 75093254

GSM3564793 ChIPSeq.HEK293_T2_B_mut 61175503

GSM3564794 ChIPSeq.HEK293_T2_Y78A_mut 68255927

GSM3564795 ChIPSeq.HEK293_T3_B_mut 68788471

GSM3564796 ChIPSeq.HEK293_T3_Y78A_mut 69951070

GSM3564797 ChIPSeq.HEK293_vec 61797238

GSM3564798 ChIPSeq.HEK293_Y78A_B_mut 68043038

GSM3564799 ChIPSeq.HEK293_F_ENL 71607516

GSM3564800 ChIPSeq.HEK293_F_T1_mut 72912339

GSM3564801 ChIPSeq.HEK293_F_T2_mut 82750115

GSM3564802 ChIPSeq.HEK293_F_T3_mut 79967093

GSM3564803 ChIPSeq.HEK293_input 82872696

GSM3564804 ChIPSeq.HK2_F_ENL 80396084

GSM3564805 ChIPSeq.HK2_F_T1_mut 62880686

GSM3564806 ChIPSeq.HK2_F_T2_mut 59955976

GSM3564807 ChIPSeq.HK2_F_T3_mut 62638629

GSM3564808 ChIPSeq.HK2_input_S31 63931469

Antibodies Antibodies used in ChIP-seq in this study: Flag (Sigma, F1804), CDK9 (Santa Cruz, sc-13130), Pol II S2P (Abcam, ab5095), and

H3K79me2 (Abcam, ab3594), and more detailed in Supplementary Method and Supplementary Tables

Peak calling parameters bowtie hg19 -v 1 -r --best --strata -m 1 -p 8 *.seq *.bowtie

macs14 -t *.bed -c Input.bed -g hs --tsize=* --wig

Data quality FASTQC 0.11.8 is run to check the sequencing quality.

Software FASTQC 0.11.8;Bowtie1 v1.1.0; MACS (version 1.4.2); R package VennDiagram v1.6;deepTools v2.0

edgeR 3.26.0.