{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Masa Roller"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14454"],"description":["This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse and rat livers with cellular processes such as replication, transcription, and the interactions of DNA with proteins. Data are available for the following laboratory strains of mouse and rat: Mus musculus (C57BL/6J and C3H), Mus musculus castaneous (CAST), Mus caroli (CAROLI), and Rattus norvegicus (F344). Liver samples from untreated mice (postnatal day 15, P15) and rats (postnatal day 56, P56) were isolated and flash-frozen. ChIP-seq was performed to identify histone modification (H3K4me3 and H3K27ac) and CTCF binding sites in livers of ten pooled individuals (mice) or one individual (rat). The experiment was done with at least three biological replicates, plus matched input libraries. Data for CTCF binding in C3H mice is available at ArrayExpress (E-MTAB-11959)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Livers (ten livers pooled for mouse or one liver for rat) were homogenised, washed twice with PBS, and lysed according to published protocols (Schmidt et al. 2009). Chromatin was sonicated to an average fragment length of 300 bp. Chromatin was immunoprecipitated using either 10 μl H3K4me3 antibody (mouse monoclonal, Merck Millipore 05-1339, lot 2780484); 10 μl H3K27ac antibody (rabbit polyclonal, AbCam 4729, lot GR3187598-1); 20 μl CTCF antibody (rabbit polyclonal, Merck Millipore 07-729, lot 2517762).","Library Construction - Immunoprecipitated DNA or input DNA (max 50 ng) was used for library preparation using the ThruPLEX DNA-Seq library preparation protocol (Rubicon Genomics, UK) as described previously (Aitken et al. 2018). Library fragment size was determined using a 2100 Bioanalyzer (Agilent).","Sample Collection - Livers from males were perfused in situ with PBS and then dissected, minced, cross-linked using 1% formaldehyde solution for 20 min, quenched for 10 min with 250 mM glycine, washed twice with ice-cold PBS, and tissue pellets were stored at -80°C.","Sequencing - Libraries were quantified by qPCR (Kapa Biosystems) and sequenced on a MiSeq (Illumina) to produce single-end 50 bp reads.","Sequencing - Libraries were quantified by qPCR (Kapa Biosystems) and sequenced on a HiSeq4000 (Illumina) to produce paired-end 150 bp reads."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Peaks were identified for each ChIP-seq library and input control using MACS2 (v.2.1.2) callpeak (Zhang et al. 2008) and all peaks with a q-value >0.05 were included in downstream analyses. We used the input libraries to filter spurious peaks associated with a high input signal using the GreyListChIP R package (Brown 2021). Biologically-reproducible peaks were identified by merging ChIP-seq peaks defined as above from individual replicates and selecting those that overlapped  ≥2 individual replicate peaks.","Sequence Alignment - To identify ChIP-seq positive regions, we trimmed the HiSeq sequencing reads to 50 bp and then aligned them to genome assembly  using BWA (0.7.17) (Li and Durbin 2009)  using default parameters. Uniquely mapping reads were selected for further analysis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina MiSeq","Illumina HiSeq 4000"],"study_type":["ChIP-seq"],"species":["Mus musculus"],"pubmed_authors":["Sarah Aitken","Masa Roller"],"additional_accession":[]},"is_claimable":false,"name":"ChIP-seq analysis of histone modifications and CCCTC-binding factor (CTCF) binding in the livers of five strains of mouse and rat","description":"This study aims to investigate the interactions of mutagenic lesions from diethylnitrosamine (DEN) treatment of mouse and rat livers with cellular processes such as replication, transcription, and the interactions of DNA with proteins. Data are available for the following laboratory strains of mouse and rat: Mus musculus (C57BL/6J and C3H), Mus musculus castaneous (CAST), Mus caroli (CAROLI), and Rattus norvegicus (F344). Liver samples from untreated mice (postnatal day 15, P15) and rats (postnatal day 56, P56) were isolated and flash-frozen. ChIP-seq was performed to identify histone modification (H3K4me3 and H3K27ac) and CTCF binding sites in livers of ten pooled individuals (mice) or one individual (rat). The experiment was done with at least three biological replicates, plus matched input libraries. Data for CTCF binding in C3H mice is available at ArrayExpress (E-MTAB-11959).","dates":{"release":"2026-05-07T00:00:00Z","modification":"2026-05-07T15:18:24.516Z","creation":"2024-10-04T15:27:45.741Z"},"accession":"E-MTAB-14454","cross_references":{"ENA":["ERP164728"],"Biostudies":["E-MTAB-11959"],"EFO":["EFO_0002944","EFO_0004170","EFO_0002692","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}