{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Rahul Biradar"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15832"],"description":["Single-cell RNA sequencing (scRNA-seq) was performed on longitudinal CD4⁺ T-cell samples from 11 children who later developed type 1 diabetes and 11 matched controls. Samples were collected prior to or at the time of type 1 diabetes–specific autoantibody appearance (seroconversion), between ages 3 and 24 months (n = 73 samples). CD4⁺ T cells were isolated and profiled using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1. Individual samples were labeled with unique cell hashing antibodies and pooled into multiplexed runs, with up to 10 samples (from matched case–control pairs) combined per pool. In total, 9 multiplexed pools were processed on Chromium Next GEM Chips, targeting recovery of approximately 20,000 single cells per run (CH_run2-CH_run10). cDNA and hashtag oligo libraries were generated with dual indexing and sequenced on an Illumina NovaSeq 6000. Raw sequencing data were processed with the Cell Ranger pipeline, and computational demultiplexing was performed to assign each cell to its original sample. Downstream analysis identified 10 CD4⁺ T-cell subtypes across ~99,000 high-quality cells. No significant differences in cell-type proportions were observed between case and control pairs at individual time points. However, cell type–specific gene expression changes and enriched pathways were detected in specific cell types in cases. These early transcriptional and regulatory alterations in CD4⁺ T cells provide a valuable resource for understanding disease initiation and developing predictive biomarkers for type 1 diabetes."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - CD4+ T cells  in gel in emersion (GEM) were lysed for reverse transcription and complimentary DNA (cDNA) amplification. Full-length cDNA along with cell barcode identifiers were PCR-amplified.","Sequencing - Sequencing of cDNA libraries was performed with Illumina NovaSeq 6000 at sequencing depth of 20,000 and 5,000 reads per cell for gene expression and cell hashtag libraries, respectively.","Sample Collection - PBMC samples stored at -150°C were thawed quickly in a 37°C water bath and quantitated for cell numbers and viability using trypan blue staining with a Countess cell counter (ThermoFischer Scientific). On average, 94% of cells were viable. Dynabeads™ CD4+-positive isolation kit (Invitrogen #11331D) was used to enrich CD4+ T cells. Each individual time-point CD4+ T cells was stained using BioLegend's human Totalseq B cell hash antibody. At most 10 samples with respective cell hash antibodies stained separately. Roughly, 0.1 million cells from each stained sample was pooled as one multiplexed sample and loaded onto Chromium Next GEM Chip G. For each run, we aimed at a recovery of 20,000 single cells by super-loading 33,000 cells at a cell concentration recommended by 10X Genomics.","Library Construction - Libraries were prepared according to manufacturer's instructions using 10X Genomics Single cell 3’ Reagent Kit V3.1.  Full-length cDNA along with cell barcode identifiers were PCR-amplified. Two different cDNA sequencing libraries were prepared from reverse-transcribed polyadenylated transcripts of each cell and from cell hashtag oligo bound to the same cell, respectively, utilizing dual indexing."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The submitted count data has not been normalised."],"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":["Rahul Biradar"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA-seq analysis of longitudinal CD4+ T-cell samples reveals cell-type-specific changes during early stages of type 1 diabetes","description":"Single-cell RNA sequencing (scRNA-seq) was performed on longitudinal CD4⁺ T-cell samples from 11 children who later developed type 1 diabetes and 11 matched controls. Samples were collected prior to or at the time of type 1 diabetes–specific autoantibody appearance (seroconversion), between ages 3 and 24 months (n = 73 samples). CD4⁺ T cells were isolated and profiled using the 10x Genomics Chromium Single Cell 3′ Reagent Kits v3.1. Individual samples were labeled with unique cell hashing antibodies and pooled into multiplexed runs, with up to 10 samples (from matched case–control pairs) combined per pool. In total, 9 multiplexed pools were processed on Chromium Next GEM Chips, targeting recovery of approximately 20,000 single cells per run (CH_run2-CH_run10). cDNA and hashtag oligo libraries were generated with dual indexing and sequenced on an Illumina NovaSeq 6000. Raw sequencing data were processed with the Cell Ranger pipeline, and computational demultiplexing was performed to assign each cell to its original sample. Downstream analysis identified 10 CD4⁺ T-cell subtypes across ~99,000 high-quality cells. No significant differences in cell-type proportions were observed between case and control pairs at individual time points. However, cell type–specific gene expression changes and enriched pathways were detected in specific cell types in cases. These early transcriptional and regulatory alterations in CD4⁺ T cells provide a valuable resource for understanding disease initiation and developing predictive biomarkers for type 1 diabetes.","dates":{"release":"2025-10-31T00:00:00Z","modification":"2026-05-27T13:54:40.99Z","creation":"2025-10-24T13:39:59.416Z"},"accession":"E-MTAB-15832","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}