Nature - USA (2020-01-23)

5

nature research | reporting summary

October 2018

GSM3983234 mouse-active-T-cell-siH2A.Z-Rnase-treated-NS

GSM3993419 hela-WT-input

Genome browser session

(e.g. UCSC)

Not used

Methodology

Replicates BrdU, ORC1 and Histone ChIP-seq experiments were performed in duplicates with an input control for each experiment.

Nascent strand (NS) seq experiments were performed in duplicates with an input control for each experiment.

Sequencing depth hela-WT-H2A.Z_rep1, single-end, read number: 29217798, read length: 50 bp

hela-WT-H2A.Z_rep2, single-end, read number: 36786000, read length: 50 bp

hela-H2A.Z-KD-H2A.Z_rep1, single-end, read number: 30506757, read length: 50 bp

hela-H2A.Z-KD-H2A.Z_rep2, single-end, read number: 30327697, read length: 50 bp

hela-WT-H4K20me1_rep1, single-end, read number: 27007998, read length: 50 bp

hela-WT-H4K20me2_rep1, single-end, read number: 46342466, read length: 50 bp

hela-WT-H4K20me2_rep2, single-end, read number: 21530865, read length: 50 bp

hela-WT-H4K20me3_rep1, single-end, read number: 35063713, read length: 50 bp

hela-WT-input_rep1, single-end, read number: 35063713, read length: 50 bp

hela-WT-input_rep2, single-end, read number: 30813565, read length: 50 bp

hela-H2A.Z-KD-input_rep1, single-end, read number: 33781291, read length: 50 bp

hela-H2A.Z-KD-input_rep2, single-end, read number: 31197655, read length: 50 bp

hela-H2A.Z-KD-H4K20me1_rep1, single-end, read number: 33187537, read length: 50 bp

hela-H2A.Z-KD-H4K20me2_rep1, single-end, read number: 41079876, read length: 50 bp

hela-H2A.Z-KD-H4K20me2_rep2, single-end, read number: 22572525, read length: 50 bp

hela-H2A.Z-KD-H4K20me3_rep1, single-end, read number: 32816918, read length: 50 bp

hela-WT-ORC1_rep1, single-end, read number: 26780831, read length: 50 bp

hela-WT-ORC1_rep2, single-end, read number: 27504126, read length: 50 bp

hela-H2A.Z-KD-ORC1_rep1, single-end, read number: 39982452, read length: 50 bp

hela-H2A.Z-KD-ORC1_rep2, single-end, read number: 21389952, read length: 50 bp

hela-WT-NS_rep1, single-end, read number: 22799872, read length: 50 bp

hela-WT-NS_rep2, single-end, read number: 24639890, read length: 50 bp

hela-WT-Rnase-treated-NS_rep1, single-end, read number: 18786498, read length: 50 bp

hela-WT-Rnase-treated-NS_rep2, single-end, read number: 53131336, read length: 51 bp

hela-WT-genome-NS_rep1, single-end, read number: 16940577, read length: 50 bp

hela-WT-genome-NS_rep2, single-end, read number: 36229449, read length: 50 bp

hela-H2A.Z-KD-NS_rep1, single-end, read number: 33595669, read length: 50 bp

hela-H2A.Z-KD-Rnase-treated-NS_rep1, single-end, read number: 23120958, read length: 50 bp

hela-H2A.Z-KD-genome-NS_rep1, single-end, read number: 25083887, read length: 50 bp

hela-WT-BrdU-10min_rep1, single-end, read number: 35791042, read length: 50 bp

hela-WT-BrdU-10min_rep2, single-end, read number: 23413789, read length: 50 bp

hela-WT-BrdU-1h_rep1, single-end, read number: 42484612, read length: 50 bp

hela-WT-BrdU-3h_rep1, single-end, read number: 33748760, read length: 50 bp

hela-WT-BrdU-6h_rep1, single-end, read number: 21086656, read length: 50 bp

hela-H2A.Z-KD-10min_rep1, single-end, read number: 41527806, read length: 50 bp

hela-H2A.Z-KD-10min_rep2, single-end, read number: 24074710, read length: 50 bp

hela-H2A.Z-KD-1h_rep1, single-end, read number: 47490348, read length: 50 bp

hela-H2A.Z-KD-3h_rep1, single-end, read number: 25062487, read length: 50 bp

hela-H2A.Z-KD-6h_rep1, single-end, read number: 19341066, read length: 50 bp

hela-WT-RNA-seq, pair-end, read number: 41904139, read length: 150 bp

hela-H2A.Z-KD-RNA-seq, pair-end, read number: 44240416, read length: 150 bp

mouse-active-T-cell-WT-H4K20me2, single-end, read number: 28935057, read length: 50 bp

mouse-active-T-cell-H2A.Z-cKO-H4K20me2, single-end, read number: 24039043, read length: 50 bp

mouse-active-T-cell-WT-input, single-end, read number: 24703906, read length: 50 bp

mouse-active-T-cell-H2A.Z-cKO-input, single-end, read number: 28063843, read length: 50 bp

mouse-active-T-cell-WT-NS, pair-end, read number: 41513960, read length: 150 bp

mouse-active-T-cell-H2A.Z-cKO-NS, pair-end, read number: 47561656, read length: 150 bp

mouse-active-T-cell-WT-NS, pair-end, read number: 62444070, read length: 150 bp

mouse-active-T-cell-H2A.Z-cKO-NS, pair-end, read number: 57631120, read length: 150 bp

Antibodies Anti-H2A.Z ,Abcam, ab4174; Anti-H4K20me1, Abcam, ab9051; Anti-H4K20me2, Abcam, ab9052; Anti-H4K20me3, Abcam,

ab9053; Anti-BrdU, BD, BD44. The ORC1 chip used the M-280 streptavidin dynabead.

Peak calling parameters Reads were uniquely mapped to genome using bowtie2. Peaks were called using MACS (--shiftsize=75) and PeakSeq (fdr

below 0.5%)

Data quality Read with high quality were retained using Fastx_toolkit, unique reads were used for peak calling with FDR below 0.5%

Software Bowtie v2.2.5, bedtools v2.17.0, R v3.4.3, MACS v1.4.1, python v2.7.6, tophat v2.2.1, cufflinks v2.2.1, samtools v1.2.1,

deeptools v2.3.5, IGV v2.3, PeakSeq v1.3, FASTX-Tools v 0.0.13,