biostudies-arrayexpressFeras MachourHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16861Map LSM4 binding to chromatin at DNA double-strand breaks (DSBs) induced by AsiSI endonuclease in U2OS-DIvA cells.biostudies-arrayexpressNucleic Acid Extraction - Cells were fixed with 1% PFA for 10 minutes at room temperature, and cross-linking was stopped with 0.125 M Glycine for 5 min. After cell lysis, DNA was sheared to the size of 300–500 bp using a Vibra cell sonicator (15 sec ON, 30 sec OFF, 35% duty, 20 cycles). Five percent of each supernatant was used as input control and processed with the cross-linking reversal step. Chromatin was immunoprecipitated using 2ug of the indicated antibodies and Protein A/G magnetic beads. Following reverse cross-linking; the precipitated DNA was purified using the Macherey-Nagel Nucleospin kitGrowth Protocol - U2OS-DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10 % heat-inactivated fetal bovine serum (Gibco), 2mM L-glutamine (Gibco), 100unit/mL penicillin, 100μg/mL streptomycin (Gibco) and 1mM Sodium Pyruvate in the presence of 400μg/mL G418 at 37°C and 5% CO2.Library Construction - Chip-seq libraries were prepared at the Crown Genomics institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science starting from 1-20ng of DNA as previously described (Blecher-Gonen R et al. Nat. prot. (2013)). Libraries were quantified by Qubit (Thermo fisher scientific) and TapeStation (Agilent). Libraries average peak size was ~500bp.Sequencing - Sequencing was done on the NovaSeq6000 sequencing platform (Illumina) using an S1 mode, 100 cycles kit, allocating ~ 40M reads per sample (single end sequencing).Sample Collection - U2OS DiVA cells were plated at 15cm and allowed to reach 80% confluency before treatment/collectionSample Treatment - Cells were treated with 300nM 4OH for 4 hrs to induce AsiSI-dependent DSBs.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Coverage bigWig files from biological replicates were merged using bigwigCompare with the 'add' operation. Average log2 ratios between −4-OHT and +4-OHT conditions were computed using bigwigCompare with the 'log2' operation. Averaged ChIP-seq log2 profiles around AsiSI sites in transcriptionally active or silent/intergenic regions (as defined in Saur et al., 2025) were computed using computeMatrix (deepTools) with 500 bp smoothing bins in a 5 kb window.Sequence Alignment - ChIP-seq samples were aligned to the GRCh38/hg38 human genome assembly using Bowtie2 (Langmead and Salzberg, 2012). Aligned reads were converted to BAM format and sorted, indexed, and quality-filtered using SAMtools (Li et al., 2009). Coverage tracks were generated using bamCoverage (deepTools) (Ramírez et al., 2016) with RPKM normalization.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ChIP-seqHomo sapiensFeras MachourfalseChIP-seq for LSM4 in U2OS-DIvA cells -/+ AsiSI-induction by 4OHTMap LSM4 binding to chromatin at DNA double-strand breaks (DSBs) induced by AsiSI endonuclease in U2OS-DIvA cells.2026-04-30T00:00:00Z2026-04-30T01:02:07.213Z2026-04-07T11:17:57.346ZE-MTAB-16861ERP191811EFO_0002944EFO_0004170EFO_0003789EFO_0002692EFO_0004917EFO_0005518EFO_0003816EFO_0004184EFO_0003969