biostudies-arrayexpressMilita DarguzyteMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17275Comparing human T cell repertoire development in humanized mice using CD34+ cell transplantation in NSG strain versus NSG without murine MHC (DKO). Additionally, comparing two preconditioning protocols: busulfan (BU) versus irradiation (IR). In total 4 groups compared: DKO-BU, DKO-IR, NSG-BU and NSG-IR. 3 CB donors were used to humanize these mice.biostudies-arrayexpressSample Collection - Spleens harvested from mice and smashed to single cell suspension. The CD3+ Cell isolation done using Miltenyi kit.Nucleic Acid Extraction - Single cells were isolated via the Single-Cell Capture and cDNA Synthesis with the BD Rhapsody Express Single-Cell Analysis System according to the manufacturer’s recommendations (BD Biosciences, 23-22952(02)) using the BD Rhapsody Cartridge Kit (BD Biosciences, cat. no. 664887) and the BD Rhapsody cDNA Kit (BD Biosciences, cat. no. 633773).Library Construction - Whole transcriptome, sample tag, and TCR/BCR libraries were prepared using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit (BD Biosciences, cat. no. 633801) and the BD Rhapsody TCR/BCR Amplification Kit (BD Biosciences, cat. no. 665345) following the BD Rhapsody System TCR/BCR full length, mRNA WTA and Sample Tag Library Preparation Protocol (BD Biosciences, 23-24018(03)).Sequencing - Libraries were sequenced on an Illumina NovaSeq X platform in paired mode with a read configuration of 86 bp for read 1 and 216 bp for read 2, using NovaSeq X 10B Reagent Kit (300 cycles) chemistry.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesData Transformation - aw sequencing reads were demultiplexed using Bcl2fastq2 (v2.20) and processed through the BD Rhapsody Sequence Analysis Pipeline (v2.2), which aligned reads to the GRCh38/hg38 reference genome (GENCODE annotation, RhapRef_Human_WTA_2023-02) and generated per-cell UMI-based molecular count matrices. Hashtag oligonucleotide (HTO) counts were normalized for sample demultiplexing, and only singlet cells were retained for downstream analysis. Low-quality cells were excluded based on per-sample thresholds for the number of detected genes and the percentage of mitochondrial reads. Ribosomal genes (both small and large subunit) and mitochondrial genes (MT- prefix) were removed prior to normalization. Gene expression counts were normalized using the LogNormalize method, which divides each cell's raw UMI counts by the total counts for that cell, multiplies by a scale factor of 10,000, and applies a natural log transformation (log1p), as implemented in the Seurat (v5.3.0) NormalizeData function.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNA from single cellsMus musculusJonas Schulte-SchreppingJan-Malte KleidMilita DarguzytefalseSingle cell RNA seq of human CD3+ splenocytes from humanized miceComparing human T cell repertoire development in humanized mice using CD34+ cell transplantation in NSG strain versus NSG without murine MHC (DKO). Additionally, comparing two preconditioning protocols: busulfan (BU) versus irradiation (IR). In total 4 groups compared: DKO-BU, DKO-IR, NSG-BU and NSG-IR. 3 CB donors were used to humanize these mice.2026-07-12T00:00:00Z2026-07-12T01:00:52.389Z2026-07-02T12:05:31.571ZE-MTAB-17275ERP196084EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184