biostudies-arrayexpressStijn VerwaerdeMus musculusChromatinHDbowtie2https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16048ATAC-sequencing of murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.biostudies-arrayexpressSequencing - Libraries were sequenced on NovaSeq 6000 (Illumina) to generate paired 50-bp reads.Library Construction - Transposed DNA was amplified using a NEBNext High Fidelity 2× PCR Master Mix (New England Biolabs) with indexed primers. Libraries were purified using SPRIselect beads (Beckman Coulter) to remove primer dimers.Sample Collection - Alveolar macrophages were collected by bronchoalveolar lavage (BAL). Single-cell suspension was stained with monoclonal antibodies followed by cell sorting. Additional information can be found in original publication.Nucleic Acid Extraction - ATAC-seq was carried out with minor adaptations from the protocol described in the following reference: \"Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: A method for assaying chromatin accessibility genome-wide. Curr Protoc Mol Biol 2015, 21.29.1-21.29.9 (2015).\" Additional information can be found in original publication.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data were normalized based on library size and further analysis was performed using ChromatinHD.Sequence Alignment - Mapping was performed to a mouse reference genome (mm39) with bowtie2 (v2.5.3). Duplicated reads and non-aligned reads were removed from the final bam files.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000ATAC-seqMus musculusType-2 Innate Lymphocytes Trigger an Inflammatory Switch in Alveolar MacrophagesStijn VerwaerdeJean-François HastirStijn Verwaerde, Jean-François Hastir, Sjoerd Schetters, Ursula Smole, Leen Seys, Antonio P. Baptista, Kieran English, Martijn J. Schuijs, Helena Aegerter, Karel FA Van Damme, Aimée Bugler-Lamb, Nikita Gerebtsov, Wendy Toussaint, Tatsuma Ban, Tomohiko Tamura, Florent Ginhoux, Zhaoyuan Liu, Wouter Saelens, Hamida Hammad, Martin Guilliams, Bart N. Lambrecht1, 2,8falseATAC-sequencing of murine alveolar macrophages after IL-33 treatmentATAC-sequencing of murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.2025-12-12T00:00:00Z2026-05-27T12:48:33.534Z2025-11-13T14:20:35.27ZE-MTAB-16048ERP184015EFO_0002944EFO_0007045EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0004184