{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Stijn Verwaerde"],"organism":["Mus musculus"],"software":["bowtie2","DiffBind"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16047"],"description":["CUT&RUN of IRF4 in murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["CUT&RUN"],"species":["Mus musculus"],"pubmed_title":["Type-2 Innate Lymphocytes Trigger an Inflammatory Switch in Alveolar Macrophages"],"pubmed_authors":["Stijn Verwaerde","Jean-François Hastir","Stijn 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, 2,8"],"additional_accession":[]},"is_claimable":false,"name":"IRF4 CUT&RUN sequencing of murine alveolar macrophages after IL-33 treatment","description":"CUT&RUN of IRF4 in murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.","dates":{"release":"2025-12-12T00:00:00Z","modification":"2026-04-17T17:06:39.702Z","creation":"2025-11-13T14:14:29.116Z"},"accession":"E-MTAB-16047","cross_references":{"ENA":["ERP184014"],"EFO":["EFO_0002944","EFO_0009973","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}