biostudies-arrayexpressMus musculuscutadapt (v2.6) ; bwa (0.7.17) ; Picard (2.23.8)MACS (v2.1.2)https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14144Liver samples were isolated from postnatal day 15 (P15) untreated mice and then flash frozen: Mus musculus musculus (C57BL/6J), Mus musculus castaneus (CAST), and Mus caroli (CAROLI). DEN-induced liver tumours and background liver tissue were collected from 37-week old C57BL/6J mice. ATAC-seq was performed to identify the open regions of the genome.biostudies-arrayexpressSample Treatment - No diethylnitrosamine treatment was administered to animalsNucleic Acid Extraction - Samples were treated as previously described in Omni-ATAC protocol (Corces et al. 2017), with minor modifications to the nuclear isolation steps (in Step 1, 1 ml of 1× homogeniser buffer was used instead of 2 ml; in Step 4, douncing was performed with 30 strokes instead of 20).Sample Treatment - A subgroup of C57BL/6J mice were treated with a single intraperitoneal dose of diethylnitrosamine (20 mg/kg) on post-natal day 15 (P15) to induce liver tumours, which were isolated on day P252. Background liver tissue was also collected.Sequencing - Pooled libraries were sequenced on a NovaSeq6000 (Illumina) to produce paired-end 50 bp reads, according to manufacturer’s instructions.Library Construction - ATAC-seq was performed as described previously (Corces et al. 2017).Sample Collection - Livers from mice were isolated and flash frozen at -80°C.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesSequence Alignment - Adaptor sequences were removed using cutadapt (v.2.6) (Martin 2011). Reads were aligned to the corresponding reference genomes Ensembl v.91 (BL6 = GRCm38, CAST = CAST_EiJ_v1, CAROLI = CAROLI_EiJ_v1.1) using bwa (v.0.7.17) (Li and Durbin 2009). Data from multiple lanes were merged prior to deduplication; duplicates were marked using Picard (v.2.23.8) (Broad Institute 2019). Alignment filtering was performed with samtools (v.1.9) and reads overlapping regions with abnormal read coverage were removed. Reads aligning to mitochondrial DNA were excluded from further analysis. Read positions aligning to + and - strands were offset by +5bp and -4bp, respectively, to represent the middle of the transposition event, as described previously (Buenrostro et al. 2013).Data Transformation - Peaks were called using MACS2 (v.2.1.2) (Zhang et al. 2008) from insets (here inset refers to genomic coordinates between 5' ends of read pairs from paired-end sequencing). This was done for each sample individually and for an inset pool containing all replicates (macs2 callpeak -f BEDPE --keep-dup all -B --SPMR -p 0.01 --nomodel -g mm --keep-dup all). Lower p-value threshold was used, as peaks were used as input into Irreproducibility Discovery Rate (IDR) analysis (Li et al. 2011))MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ATAC-seqMus musculusE-MTAB-11780Sarah AitkenMartin TaylorDuncan OdomLana TalmanefalseATAC-seq of C57BL/6J, Castaneus, and Caroli mouse livers and C57BL/6J liver tumoursLiver samples were isolated from postnatal day 15 (P15) untreated mice and then flash frozen: Mus musculus musculus (C57BL/6J), Mus musculus castaneus (CAST), and Mus caroli (CAROLI). DEN-induced liver tumours and background liver tissue were collected from 37-week old C57BL/6J mice. ATAC-seq was performed to identify the open regions of the genome.2026-05-15T00:00:00Z2026-05-15T10:52:34.224Z2024-06-04T11:41:29.623ZE-MTAB-14144ERP160849E-MTAB-11780EFO_0002944EFO_0007045EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0003969EFO_0004184