{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Stijn Verwaerde"],"organism":["Mus musculus"],"software":["ChromatinHD","bowtie2"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16048"],"description":["ATAC-sequencing of murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data 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."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["ATAC-seq"],"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":"ATAC-sequencing of murine alveolar macrophages after IL-33 treatment","description":"ATAC-sequencing of murine alveolar macrophages after 3 I.T. doses of PBS (control) or IL-33 treatment.","dates":{"release":"2025-12-12T00:00:00Z","modification":"2026-05-27T12:48:33.534Z","creation":"2025-11-13T14:20:35.27Z"},"accession":"E-MTAB-16048","cross_references":{"ENA":["ERP184015"],"EFO":["EFO_0002944","EFO_0007045","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}