biostudies-arrayexpressStijn VerwaerdeMus musculusbowtie2DiffBindhttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16047CUT&RUN of IRF4 in murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.biostudies-arrayexpressLibrary Construction - Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. Cleanup of libraries was performed with AMPure XP beads (Beckman Coulter).Sequencing - Libraries were sequenced on NovaSeq 6000 (Illumina) to generate paired 50-bp reads.Nucleic Acid Extraction - CUT and RUN was carried out with minor adaptations from the protocol described in the following reference: \"Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat Protoc 13, 1006–1019 (2018)..\" Additional information can be found in original publication.Sample Collection - Alveolar macrophages were collected by bronchoalveolar lavage (BAL). BAL was lightly fixed with formaldehyde (final concentration of 0.1%) quenched with glycine and single-cell suspension was stained with monoclonal antibodies followed by cell sorting. Additional information can be found in original publication.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - Data were normalized based on carry-over of E. coli DNA from purification of pA/MNase. Normalization step a was performed with the DiffBind package.Sequence Alignment - Mapping was performed to a mouse reference genome (mm39) with bowtie2 (v2.5.3). The bam files were ordered and filtered to contain fragments with lenght ≤150 bp. The filtered and sorted bam files were used for further analysis. For normalization purpose, bam files with the sequences mapped to E.coli reference genome (eschColi_K12) were also generated.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000CUT&RUNMus 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, 2,8falseIRF4 CUT&RUN sequencing of murine alveolar macrophages after IL-33 treatmentCUT&RUN of IRF4 in murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.2025-12-12T00:00:00Z2026-04-17T17:06:39.702Z2025-11-13T14:14:29.116ZE-MTAB-16047ERP184014EFO_0002944EFO_0009973EFO_0004170EFO_0004917EFO_0005518EFO_0003816EFO_0004184