{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Stijn Verwaerde"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Mus musculus musculus"],"species":["Mus musculus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16590"],"description":["Single cell sequencing dataset of CD45+ and CD45- lung cells in a timecourse after intratracheal diphtheria toxin treatment in the SPAM-deleter model. Sequencing data was obtained at following timepoints: 0h, 12h, 24h, 2 days, 5 days, 8 days and 14 days."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - The DNA libraries were prepared using the GemCode Single Cell 5′ Gel Bead and Library kit, version Next GEM v2 according to the manufacturer's instructions (10x Genomics, User Guide CG000330). Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 5′ gene expression and cell surface protein construction. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent).","Sample Collection - 4 untreated (0h) or DTx treated SPAM deleter mice were sacrificed and lung single cell suspensions were created. The cells were incubated with fluorophore labeled antibodies for FACS and TotalSeq C library for 30 minutes on 4°C. 30000 CD45-, 15000 CD45+CD64+ and 15000 CD45+CD64- cells per biological replicate were FACS sorted. Cells were pooled in the same eppendorf tube, diluted into a final concentration of 2000 cells/ μl and loaded on the 10X chromium device.","Nucleic Acid Extraction - The DNA libraries were prepared using the GemCode Single Cell 5′ Gel Bead and Library kit, version Next GEM v2 according to the manufacturer's instructions (10x Genomics, User Guide CG000330). Size selection with SPRIselect Reagent Kit (Beckman Coulter, B23318) was used to separate amplified cDNA molecules for 5′ gene expression and cell surface protein construction. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using the 2100 BioAnalyzer (Agilent).","Sequencing - NovaSeq6000 paired sequencing 28-10-10-90 (R1-I1-I2-R2)  (+ 1% PhiX)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Stijn Verwaerde","Bart Lambrecht"],"additional_accession":[]},"is_claimable":false,"name":"single cell RNA sequencing of murine lungs of SPAM deleter mice after alveolar macrophage depletion","description":"Single cell sequencing dataset of CD45+ and CD45- lung cells in a timecourse after intratracheal diphtheria toxin treatment in the SPAM-deleter model. Sequencing data was obtained at following timepoints: 0h, 12h, 24h, 2 days, 5 days, 8 days and 14 days.","dates":{"release":"2026-02-12T00:00:00Z","modification":"2026-02-12T14:22:30.926Z","creation":"2026-02-10T12:48:05.882Z"},"accession":"E-MTAB-16590","cross_references":{"ENA":["ERP188938"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}