biostudies-arrayexpressNeus VisaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17179CUT&Tag was performed to identify the effect of DIS3 depletion on DNA:RNA hybrids genome-wide. DIS3-AID HCT116 cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control). CUT&Tag was performed targeting DNA:RNA hybrids using the CUT&Tag-IT® R-loop Assay Kit (Active Motive) with the S9.6 antibody.biostudies-arrayexpressSample Collection - DIS3-AID HCT116 human cell line from Davidson et al. (doi: 10.1016/j.celrep.2019.02.012). DIS3-AID cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control). CUT&Tag was performed using CUT&Tag-IT® R-loop Assay Kit (Active Motif, cat. no. 53167) according to manufacturer's instructions.Growth Protocol - Cells were cultured at 37°C in a humidified incubator with 5% CO2, in DMEM supplemented with Penicillin and Streptomycin and 10% of heat-inactivated fetal bovine serum.Nucleic Acid Extraction - The DNA was extracted using SPRI beads provided as kit component.Sequencing - Samples were sequenced on a Nextseq 2000 P3 100 Flowcell.Sample Treatment - DIS3-AID cells were treated with either 500 μM Auxin or DMSO.Library Construction - Q5 Polymerase master mix was used for library enrichment, using uniquely barcoded i5 and i7 primers.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The CPM normalization was performed using the nf-core cutandrun pipeline (v3.2.2).Sequence Alignment - CUT&TAG data was preprocessed using the nf-core cutandrun pipeline (v3.2.2) using the following parameters: nextflow run nf-core/cutandrun \ -r 3.2.2 \ --input samplesheet_18exp.csv \ --genome hg38 \ --spikein_genome dm6 \ --igenomes_base /sw/data/igenomes \ --use_control false \ --peakcaller macs2 \ --macs2_narrow_peak true \ --macs2_qvalue 0.05 \ --blacklist \"${PWD}/hg38-blacklist.v2.bed\" \ --consensus_peak_mode group \ --replicate_threshold 2 \ BAM files were converted to bigWig files using bamCoverage.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000CUT&TagHomo sapiensShruti JainNeus VisafalseCUT&Tag for S9.6 in DIS3-depleted cellsCUT&Tag was performed to identify the effect of DIS3 depletion on DNA:RNA hybrids genome-wide. DIS3-AID HCT116 cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control). CUT&Tag was performed targeting DNA:RNA hybrids using the CUT&Tag-IT® R-loop Assay Kit (Active Motive) with the S9.6 antibody.2026-08-03T00:00:00Z2026-08-03T10:02:49.21Z2026-06-17T14:47:02.269ZE-MTAB-17179ERP195285EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969