biostudies-arrayexpressRaphael CarapitoMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17643Protein prenylation is essential for membrane targeting of signaling and trafficking proteins. We identified a recurrent homozygous RABGGTA missense variant (L235F) in 23 patients from 19 consanguineous families with a severe multisystem disorder characterized by bicytopenia, recurrent infections, systemic inflammation, and life-threatening bleeding. The variant destabilized Rab geranylgeranyltransferase, resulting in widespread Rab hypoprenylation, mislocalization, and defective vesicular trafficking. RABGGTA deficiency impaired megakaryocyte maturation, platelet granule biogenesis and aggregation, as well as cytotoxic lymphocyte function, leading to macrothrombocytopenia and HLH-like inflammation. Transcriptomic and proteomic analyses revealed broad dysregulation of vesicular trafficking and stress-response pathways. Complete Rabggta loss was embryonic lethal in mice, whereas hypomorphic gunmetal mice recapitulated key hematologic and inflammatory features of the human disease. RABGGTA deficiency therefore defines the first Mendelian disorder of protein prenyltransferase function in humans and reveals Rab prenylation as a critical regulator of platelet and immune homeostasis. The present dataset corresponds to single-cell RNA sequencing of FACS-sorted CD41+ bone marrow cells from WT and gunmetal mice.biostudies-arrayexpressSample Collection - For single-cell RNA sequencing, bone marrow cells were harvested by gentle flushing of the long bones (femurs and tibiae) and pelvis with PBS supplemented with 2 mM EDTA and 3 % fetal calf serum (FCS), mechanically dissociated by pipetting using wide-bore pipette tips to minimize mechanical stress, and filtered through a 100 µm cell strainer to obtain a single-cell suspension. Bone marrow cells were then centrifuged (300 x g for 5 minutes) and incubated with rat anti-CD16/32 antibodies (1:100, clone 93, Biolegend, San Diego, CA, USA) to block Fc receptors. They were further stained with a panel of biotinylated rat antibodies against Gr1 (1:500, clone RB6-8C5, Biolegend), B220 (1:500, clone RA3-6B2, Biolegend), Mac1 (1:500, clone M1/70, Biolegend), CD3e (1:500, clone 17A2, Biolegend), CD4 (1:500, clone GK1.5, Biolegend), CD5 (1:500, clone 53-7.3, Biolegend), CD8 (1:500, clone 53-6.7, Biolegend) and TER119 (1:500, clone TER-119, Biolegend), then lineage-depleted using magnetic Dynabeads Sheep anti-Rat IgG (2 beads per target cell; Invitrogen, Thermo Fisher Scientific, Vilnius, Lithuania). The lineage-depleted fraction was centrifuged (300 x g for 5 minutes) and stained with rat anti-mouse CD41 antibodies (1:100, clone MWReg30, Biolegend), Streptavidin-PE (1:500) to exclude any residual lineage-positive cells, and DAPI (1:36000) to exclude dead cells. Viable Lineage-CD41+ cells (containing predominantly megakaryocytes) were then sorted on a BD FACSAria using a 130 µm nozzle at a low flow rate to minimize mechanical stress, collected into PBS supplemented with 2 mM EDTA and 3% FCS, and fixed using the Evercode Low Input Cell Fixation kit (Parse Biosciences).Nucleic Acid Extraction - Fixed cells were processed directly using the Parse Biosciences Evercode Whole Transcriptome workflow. Following in situ combinatorial barcoding, cells were lysed and barcoded cDNA was captured and purified according to the manufacturer's instructions.Sequencing - Libraries were paired-end sequenced on a NextSeq 2000 instrument (Illumina, San Diego, CA) according to the manufacturer’s guidelines with a sequencing depth of at least 30000 reads per cell.Library Construction - Single-cell RNA-sequencing libraries were prepared using the Parse Biosciences Evercode Whole Transcriptome (WT) kit according to the manufacturer's instructions. Fixed cells underwent in situ split-pool combinatorial barcoding, followed by cell lysis, cDNA capture and amplification, and sequencing library preparation to generate Illumina-compatible libraries.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - No normalization or expression data transformation was performed for this file. The processed data file is a sample-to-barcode mapping table provided to associate the biological samples with the Parse Evercode sample barcodes used in the experiment. The file contains biological sample metadata and corresponding sample barcode well positions and is provided as processed data because Annotare does not currently provide a dedicated category for additional mapping files.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 2000RNA-seq of coding RNA from single cellsMus musculusRaphael CarapitofalseSingle-cell RNA-seq analysis of FACS-sorted CD41+ bone marrow cells from WT and gunmetal miceProtein prenylation is essential for membrane targeting of signaling and trafficking proteins. We identified a recurrent homozygous RABGGTA missense variant (L235F) in 23 patients from 19 consanguineous families with a severe multisystem disorder characterized by bicytopenia, recurrent infections, systemic inflammation, and life-threatening bleeding. The variant destabilized Rab geranylgeranyltransferase, resulting in widespread Rab hypoprenylation, mislocalization, and defective vesicular trafficking. RABGGTA deficiency impaired megakaryocyte maturation, platelet granule biogenesis and aggregation, as well as cytotoxic lymphocyte function, leading to macrothrombocytopenia and HLH-like inflammation. Transcriptomic and proteomic analyses revealed broad dysregulation of vesicular trafficking and stress-response pathways. Complete Rabggta loss was embryonic lethal in mice, whereas hypomorphic gunmetal mice recapitulated key hematologic and inflammatory features of the human disease. RABGGTA deficiency therefore defines the first Mendelian disorder of protein prenyltransferase function in humans and reveals Rab prenylation as a critical regulator of platelet and immune homeostasis. The present dataset corresponds to single-cell RNA sequencing of FACS-sorted CD41+ bone marrow cells from WT and gunmetal mice.2026-09-28T00:00:00Z2026-09-28T01:00:37.1Z2026-09-17T15:09:08.769ZE-MTAB-17643ERP206554EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184