biostudies-arrayexpressStijn VerwaerdeMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15952Sequencing of sorted alveolar macrophages (AMs) from WT mice, or from SPAM deleter (SPecific AM deleter; Siglecf-fl-DTR-fl x Epx-Cre) mice with adoptively transferred donor AMs, treated with PBS or 3 x interleukin-33 (IL33). Experiment 1 compares AMs from PBS treated and IL-33 treated WT mice and AMs from CD45.1 WT or IRF4 -/- adoptively transferred donor AMs into IL33 treated SPAM deleter animals. Experiment 2 compares WT or Batf3 -/- adoptively transferred AMs into IL33 treated SPAM deleter animals. Experiment 3 compares AMs from house dust mite (HDM) sensitized WT mice in a timecourse during HDM challenge. Experiment 4 compares AMs from Schistosoma Mansoni (SM) sensitized WT mice in a timecourse after SM challenge. Experiment 5 compares WT or Il4ra -/- adoptively transferred AMs into IL33 treated SPAM deleter animals.biostudies-arrayexpressSample Collection - Experiment 1: WT or IRF4-/- alveolar macrophages (AMs) were culture expanded and transferred into depleted SPAM-deleter animals. After 1 week, all mice were subjected to IL-33 induced inflammation (3 consecutive doses of 100 ng intratracheally). AMs were harvested from bronchoalveolar lavage fluid 1 day after the final dose of IL-33 and FACS sorted into RLTplus buffer, supplemented with 1% βmercaptoethalol.Nucleic Acid Extraction - Qiagen RNeasy Plos Micro kit following manufacturer's instructionsSequencing - AVITI 150 cycles Cloudbreak sequencing kit single-end reads (101-10-10-0), 0.5% PhiX. The sequencing was fine and follows the standard expectations (https://www.elementbiosciences.com/products/aviti/specs) with regards to the number of reads (e.g. polonies) Passing Filter per flow cell and the %>=Q30.Sample Collection - Experiment 2: same as experiment 1, now using WT or Batf3 -/- AMsSample Collection - Experiment 3+4: AMs were harvested from bronchoalveolar lavage fluid at indicated timpoints after house dust mite challenge or schistosoma mansoni injection and FACS sorted into RLTplus buffer, supplemented with 1% βmercaptoethalol.Library Construction - Illumina stranded total RNA library prep kit was used following manufacturer's instructionSample Collection - Experiment 5: same as experiment 1, now using WT or Il4ra -/- AMsOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - To obtain FKPM values, we performed within sample normalization using full quantile normalization on bins of GC-content with the EDASeq package. We performed between-sample normalization by correcting for library size and RNA composition using full quantile normalization with the EDASeq package. To obtain the FPKM values, we divide for each sample the normalized counts by the total number of counts (in million). Then we divide for each gene the scaled counts by the gene length (in kbp). For differential gene expression analysis, we performed standard EdgeR analysis and the data was normalized by the method of trimmed mean of M-values and transformed to CPM values.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsElement AVITIRNA-seq of coding RNAMus musculusType-2 Innate Lymphocytes Trigger an Inflammatory Switch in Alveolar MacrophagesSam DupontStijn VerwaerdeBart LambrechtStijn 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, 2,8falseRNA-seq of mouse sorted alveolar macrophagesSequencing of sorted alveolar macrophages (AMs) from WT mice, or from SPAM deleter (SPecific AM deleter; Siglecf-fl-DTR-fl x Epx-Cre) mice with adoptively transferred donor AMs, treated with PBS or 3 x interleukin-33 (IL33). Experiment 1 compares AMs from PBS treated and IL-33 treated WT mice and AMs from CD45.1 WT or IRF4 -/- adoptively transferred donor AMs into IL33 treated SPAM deleter animals. Experiment 2 compares WT or Batf3 -/- adoptively transferred AMs into IL33 treated SPAM deleter animals. Experiment 3 compares AMs from house dust mite (HDM) sensitized WT mice in a timecourse during HDM challenge. Experiment 4 compares AMs from Schistosoma Mansoni (SM) sensitized WT mice in a timecourse after SM challenge. Experiment 5 compares WT or Il4ra -/- adoptively transferred AMs into IL33 treated SPAM deleter animals.2025-12-12T00:00:00Z2026-05-27T16:36:25.128Z2025-10-27T15:07:17.101ZE-MTAB-15952ERP183123EFO_0002944EFO_0004170EFO_0005518EFO_0003816EFO_0003738EFO_0004184