{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14774"],"description":["Autoimmune regulator (Aire) orchestrates the display of peripheral self-antigens to T cells developing in the thymus, thereby playing a crucial function in the induction of immune tolerance. Mice lacking Aire develop multiorgan autoimmunity, but how that reflects on immune cells in the major lymphoid organs is not well understood. Here we used single cell RNA-seq to characterize immune cells isolated from the thymus, bone marrow (BM) and lymph node (LN) of four Aire-deficient (B6.AireC313X-/-) and four wild-type (WT) mice with two male and two female mice per genotype. B6.AireC313X-/- mice were generated and kindly provided by Yael Goldfarb and Jakub Abramson (previously described in Goldfarb et.al 2021, DOI: 10.1084/jem.20201076). The mice were 6-9 weeks old at the time of sacrifice.  A total of nine sample types per individual mouse were generated in this study; immune cells isolated from three tissues; thymus, lymph node and bone marrow, where each tissue was used for GEX, TCR and BCR-seq.   Information about individual, tissue, library type and lane are indicated in the sample name as follows:  Genotype_MouseID_tissue_librarytype_lane ex. AireC313X_1_thymus_GEX_lane1"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Thymi and lymph nodes were squashed and filtered through 70 μm MACS SmartStrainers (Miltenyi Biotech, cat. 130-110-916) and washed with 0.5% fetal bovine serum (FBS; Gibco, cat. 10082147) in phosphate-buffered saline (PBS).  Bone marrow immune cells were isolated by washing with with 0.5% fetal bovine serum (FBS; Gibco, cat. 10082147) in phosphate-buffered saline (PBS) Dead dells from all three tissues were subsequently removed with Dead cell removal kit (Miltenyi Biotech, cat. 130-090-101).","Sequencing - Single cell libraries were sequenced on a NovaSeq6000 system (Illumina) by the Genomics Core Facility at the University of Bergen, using paired end sequencing, (read 1: 26bp, read 2: 90 cycles, dual index: 10bp). Libraries were quantified on a Novaseq SP-100 flow cell (Illumina, cat 20028313) and gene expression libraries were pooled 6:1 with V(D)J libraries and spiked with 1% phiX (Illumina, cat. FC-110-3001) for quality control. Sequencing was performed on a NovaSeq S4-200 flowcell (Illumina, cat. 20040719 aiming for a total of 36 000 reads per cell.","Library Construction - Ten thousand cells (counted in duplicate) from each thymus, lymph node and bore marrow sample were prepared with Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics, cat. PN-1000286) and run on the Chromium Controller (10x Genomics). Gene expression libraries were prepared using the same single cell kits, V(D)J libraries were prepared with Chromium Single Cell Mouse TCR Amplification Kit (10x Genomics, cat. PN-1000254) and Chromium Single Cell Mouse BCR Amplification Kit (10x Genomics, cat. PN-1000255) and additional Library Construction Kits (10x Genomics, cat. PN-000352)."],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"additional_accession":["ERP168642"],"pubmed_authors":["David Dolan","Adrianna Jebrzycka","Bergithe Oftedal","Lars Breivik"]},"is_claimable":false,"name":"Single cell RNA-seq of immune cells isolated from lymphoid organs of Aire-deficient and wild-type control mice","description":"Autoimmune regulator (Aire) orchestrates the display of peripheral self-antigens to T cells developing in the thymus, thereby playing a crucial function in the induction of immune tolerance. Mice lacking Aire develop multiorgan autoimmunity, but how that reflects on immune cells in the major lymphoid organs is not well understood. Here we used single cell RNA-seq to characterize immune cells isolated from the thymus, bone marrow (BM) and lymph node (LN) of four Aire-deficient (B6.AireC313X-/-) and four wild-type (WT) mice with two male and two female mice per genotype. B6.AireC313X-/- mice were generated and kindly provided by Yael Goldfarb and Jakub Abramson (previously described in Goldfarb et.al 2021, DOI: 10.1084/jem.20201076). The mice were 6-9 weeks old at the time of sacrifice.  A total of nine sample types per individual mouse were generated in this study; immune cells isolated from three tissues; thymus, lymph node and bone marrow, where each tissue was used for GEX, TCR and BCR-seq.   Information about individual, tissue, library type and lane are indicated in the sample name as follows:  Genotype_MouseID_tissue_librarytype_lane ex. AireC313X_1_thymus_GEX_lane1","dates":{"release":"2025-10-30T00:00:00Z","modification":"2025-12-09T07:34:33.841Z","creation":"2025-01-24T17:34:35.496Z"},"accession":"E-MTAB-14774","cross_references":{"ENA":["ERP168642"],"EFO":["EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}