{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Neus Visa"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17179"],"description":["CUT&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."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["CUT&Tag"],"species":["Homo sapiens"],"pubmed_authors":["Shruti Jain","Neus Visa"],"additional_accession":[]},"is_claimable":false,"name":"CUT&Tag for S9.6 in DIS3-depleted cells","description":"CUT&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.","dates":{"release":"2026-08-03T00:00:00Z","modification":"2026-08-03T10:02:49.21Z","creation":"2026-06-17T14:47:02.269Z"},"accession":"E-MTAB-17179","cross_references":{"ENA":["ERP195285"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}