{"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-16280"],"description":["CUT&Tag was performed to identify the effect of DIS3 depletion on RNAPII in response to UV irradiation. DIS3-AID HCT116 cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control) before irradiation with 8 J/m2 UVC. CUT&Tag was performed targeting RNAPII-Ser2p or RNAPII-Ser5p."],"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) before irradiation with 8 J/m2 UVC. CUT&Tag was performed targeting RNAPII-Ser2p or RNAPII-Ser5p. CUT&Tag basically as described by Kaya-Okur et al. (Doi:10.1038/s41596-020-0373-x; Doi:10.1038/s41467-019-09982-5).","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.","Sample Treatment - DIS3-AID cells were treated with either 500 μM  Auxin or DMSO before irradiation with 8 J/m2 UV-C.","Library Construction - 2x Phusion High-Fidelity PCR/GC Buffer master mix (#M0532S, NEB) was used for library enrichment, using Nextera universal i5 and uniquely barcoded i7 primers.","Nucleic Acid Extraction - The DNA was extracted using a DNA Clean & Concentrator-5 kit (#D4013, Zymo Research).","Sequencing - Samples were sequenced on  a Nextseq 2000 P2 100 Flowcell"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - CUT&TAG data was preprocessed using the nf-core cutandrun pipeline (v3.0) using the following parameters: nextflow run nf-core/cutandrun -r 3.0 SAMPLE_SHEET.csv --genome GRCh38 --use_control false --normalisation_mode CPM --peakcaller seacr,macs2 --consensus_peak_mode group --replicate_threshold 2 --minimum_alignement_q_score 20 --normalisation_binsize 1 --blacklist hg38-blacklist.v2.bed --validate_params= false. BAM files were converted to bigWig files using bamCoverage with parameters -b $FILE -o $FILE\\.scaled.bw -p max --normalizeUsing CPM and all three replicates were combined using bigWigMerge. Subsequently, bigWig files were mapped to genes using deepTools as indicated: computeMatrix scale-regions -S BIGWIG_FILE -R BED_FILE --beforeRegionStartLength 1000 --region","Data Transformation - The CPM normalization was performed using the  nf-core cutandrun pipeline (v3.0)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["CUT&RUN"],"species":["Homo sapiens"],"pubmed_authors":["Neus Visa"],"additional_accession":[]},"is_claimable":false,"name":"CUT&Tag for RNAPII-Ser2p or RNAPII-Ser5p in DIS3-depleted cells","description":"CUT&Tag was performed to identify the effect of DIS3 depletion on RNAPII in response to UV irradiation. DIS3-AID HCT116 cells were treated with either Auxin (for rapid depletion of DIS3) or DMSO (control) before irradiation with 8 J/m2 UVC. CUT&Tag was performed targeting RNAPII-Ser2p or RNAPII-Ser5p.","dates":{"release":"2026-08-03T00:00:00Z","modification":"2026-08-03T10:00:10.465Z","creation":"2025-11-25T14:57:43.007Z"},"accession":"E-MTAB-16280","cross_references":{"ENA":["ERP185576"],"EFO":["EFO_0002944","EFO_0009973","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}