{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Veronika Niederlova"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15960"],"description":["ScRNAseq data from human donors with or without T1D. Please see the associated GitHub repository for recapitulation of the analysis: https://github.com/Lab-of-Adaptive-Immunity/dia and the associated Zenodo link: 10.5281/zenodo.17280189"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - cDNA libraries were prepared using the Feature Barcode technology for Cell Surface Protein protocol (#CG000186 Rev D) with the Chromium Single Cell 5’ Library & Gel Bead and Chromium Single Cell 5' Feature Barcode Library kits (10x Genomics, #PN-1000014, #PN-1000020, #PN-1000080, #PN-1000009, #PN-1000084) according to the manufacturer's instructions.","Sequencing - Sequencing was performed on NovaSeq 6000 platform (Illumina) yielding an average of 45,745 reads per cell in the gene expression libraries and 3,712 reads per cell in the V(D)J libraries.","Sample Collection - Three to ten mL of peripheral blood were collected into EDTA-coated tubes, kept on ice, and transferred from Motol University Hospital to the Institute of Molecular Genetics within two hours. PBMCs were separated using Ficoll-Paque (GE Healthcare) and immediately frozen following a cryopreservation protocol (10x Genomics). Briefly, 4 ml of Ficoll-Paque was overlaid with blood and centrifuged at 400g for 30 minutes at room temperature (brake set to one). The mononuclear cell layer was washed in PBS and resuspended in RPMI medium containing 40% FBS. After adding an equal volume of freezing medium (RPMI, 40% FBS, and 30% DMSO), two to five aliquots of PBMCs were frozen and stored in liquid nitrogen. PBMCs were gently thawed by slow, sequential dilution in RPMI medium containing 10% FBS. To minimize cell stress, wide-bore tips were used during the thawing process. CD4+ or CD8+ T cells were sorted and processed by 10x 5' Immune Profiling scRNAseq. Cell hashing was used to distinguish donors.","Nucleic Acid Extraction - Cells from both cohorts were loaded onto a 10x Chromium machine (10x Genomics) aiming for a the yield of 1500 cells per sample."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Datasets were normalized with the default method in the Seurat 4.3.1 package (scale factor = 1 × 104)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Veronika Niederlova"],"additional_accession":[]},"is_claimable":false,"name":"ScRNAseq analysis of data from patients with T1D and healthy donors","description":"ScRNAseq data from human donors with or without T1D. Please see the associated GitHub repository for recapitulation of the analysis: https://github.com/Lab-of-Adaptive-Immunity/dia and the associated Zenodo link: 10.5281/zenodo.17280189","dates":{"release":"2025-11-13T00:00:00Z","modification":"2026-05-27T13:02:29.108Z","creation":"2025-11-12T20:54:43.37Z"},"accession":"E-MTAB-15960","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}