{"entity": "publication", "iuid": "6821d1cd51294efd9c8abd81faf7a73a", "timestamp": "2026-08-08T03:34:42.008Z", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6821d1cd51294efd9c8abd81faf7a73a"}}, "title": "Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.", "authors": [{"family": "Kumar", "given": "Banushree", "initials": "B", "orcid": "0000-0001-9200-6773", "researcher": {"href": "https://publications.scilifelab.se/researcher/2dd7494dc4ea43d9b493fd6a099fc675.json"}}, {"family": "Navarro", "given": "Carmen", "initials": "C", "orcid": "0000-0001-5438-9654", "researcher": {"href": "https://publications.scilifelab.se/researcher/85a9184774364d2592961587bdce8c85.json"}}, {"family": "Yung", "given": "Philip Yuk Kwong", "initials": "PYK", "orcid": "0000-0003-2926-6980", "researcher": {"href": "https://publications.scilifelab.se/researcher/97f9b0c8cf5a4f3ab22629842c2b08dd.json"}}, {"family": "Lyu", "given": "Jing", "initials": "J"}, {"family": "Salazar Mantero", "given": "Angelo", "initials": "A"}, {"family": "Katsori", "given": "Anna-Maria", "initials": "A"}, {"family": "Schw\u00e4mmle", "given": "Hannah", "initials": "H"}, {"family": "Martin", "given": "Marcel", "initials": "M"}, {"family": "Els\u00e4sser", "given": "Simon J", "initials": "SJ", "orcid": "0000-0001-8724-4849", "researcher": {"href": "https://publications.scilifelab.se/researcher/fcf26e35e037499aa1441a7738ba61af.json"}}], "type": "journal article", "published": "2024-10-03", "journal": {"title": "Nat Protoc", "issn": "1750-2799", "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": "ChIP-seq is a widely used technique for studying histone post-translational modifications and DNA-binding proteins. DNA fragments associated with a specific protein or histone modification epitope are captured by using antibodies, sequenced and mapped to a reference genome. Albeit versatile and popular, performing many parallel ChIP-seq experiments to compare different conditions, replicates and epitopes is laborious, is prone to experimental variation and does not allow quantitative comparisons unless adequate spike-in chromatin is included. We present a detailed protocol for performing and analyzing a multiplexed quantitative chromatin immunoprecipitation-sequencing experiment (MINUTE-ChIP), in which multiple samples are profiled against multiple epitopes in a single workflow. Multiplexing not only dramatically increases the throughput of ChIP-seq experiments (e.g., profiling 12 samples against multiple histone modifications or DNA-binding proteins in a single experiment), but also enables accurate quantitative comparisons. The protocol consists of four parts: sample preparation (i.e., lysis, chromatin fragmentation and barcoding of native or formaldehyde-fixed material), pooling and splitting of the barcoded chromatin into parallel immunoprecipitation reactions, preparation of next-generation sequencing libraries from input and immunoprecipitated DNA and data analysis using our dedicated analysis pipeline. This pipeline autonomously generates quantitatively scaled ChIP-seq tracks for downstream analysis and visualization, alongside necessary quality control indicators. The entire workflow requires basic knowledge in molecular biology and bioinformatics and can be completed in 1 week. MINUTE-ChIP empowers biologists to perform every ChIP-seq experiment with an appropriate number of replicates and control conditions, delivering more statistically robust, exquisitely quantitative and biologically meaningful results.", "doi": "10.1038/s41596-024-01058-z", "pmid": "39363107", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41596-024-01058-z"}], "notes": [], "created": "2025-02-28T14:15:54.627Z", "modified": "2025-11-28T20:16:06.367Z"}