Nature - 2019.08.29

7

nature research | reporting summary

October 2018

DD_2_PrimeView_par_Kelly_DMSO.CEL

DD_5_PrimeView_Res_Kelly_TAE.CEL

DD_6_PrimeView_Res_Kelly_TAE.CEL

DD_7_PrimeView_Res_Kelly_JQ1.CEL

DD_8_PrimeView_Res_Kelly_JQ1.CEL

Microarray_KD_Boris

Raw files:

Res_Kelly_shBORIS_1.CEL

Res_Kelly_shBORIS_2.CEL

Res_Kelly_shLUC_1.CEL

Res_Kelly_shLUC_2.CEL

10X_sens_IR_Res

Raw files:

Sens.possorted_genome_bam.bam

Intermediate_Res.possorted_genome_bam.bam

Full_Res.possorted_genome_bam.bam

Processed files:

Sens_matrix.mtx

Intermediate_Res_matrix.mtx

Full_Res_matrix.mtx

barcodes.tsv

genes.tsv

HiChIP_sens_res

Raw files:

KellyRes1_1.fastq.tar.gz

KellyRes1_2.fastq.tar.gz

KellyRes2_1.fastq.tar.gz

KellyRes2_2.fastq.tar.gz

KellyRes3_1.fastq.tar.gz

KellyRes3_2.fastq.tar.gz

KellyWTrep1_1.fastq.bz2

KellyWTrep1_2.fastq.bz2

KellyWTrep2_1.fastq.bz2

KellyWTrep2_2.fastq.bz2

KellyWTrep3_1.fastq.bz2

KellyWTrep3_2.fastq.bz2

Processed files:

Kelly-Res-SMC1.bedpe

Kelly-Res-SMC1-petcount.bedpe

Kelly-SMC1.bedpe

Kelly-SMC1-petcount.bedpe

HiChIP_KD_Boris

Raw files:

Kelly_shBORIS1_1.fastq.tar.gz

Kelly_shBORIS1_2.fastq.tar.gz

Kelly_shBORIS2_1.fastq.tar.gz

Kelly_shBORIS2_2.fastq.tar.gz

Kelly_shBORIS3_1.fastq.tar.gz

Kelly_shBORIS3_2.fastq.tar.gz

Kelly_shLUC1_1.fastq.tar.gz

Kelly_shLUC1_2.fastq.tar.gz

Kelly_shLUC2_1.fastq.tar.gz

Kelly_shLUC2_2.fastq.tar.gz

Kelly_shLUC3_1.fastq.tar.gz

Kelly_shLUC3_2.fastq.tar.gz

Processed files:

shBORIS-results.csv

shLUC-results.csv

Genome browser session

(e.g. UCSC)

No longer applicable.

Methodology

Replicates For each mark assessed, two biological replicates were performed. All ChIP-seq data are derived from the analysis of both

replicates.

Sequencing depth ChIP-seq libraries were generated using the NEBNext Ultra II DNA Library Prep kit (E7645), following the manufacturer's

instructions. Starting DNA material ranged from 2.5 to 10ng, and PCR amplification (8 to 10 cycles) was performed using

NEBNext Multiplex Oligos for Illumina (E7335 and E7500) with distinct indices to allow for multiplexing of up to 12 samples

to be run on the Illumina NextSeq 500 for 75 bases in single-read mode.

Sample Total_reads Uniquely_mapped_reads

Par_BORIS_1.fastq.gZ 52592735 39434783

Par_BORIS_2.fastq.gz 54031826 40040869