biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsRaphael CarapitoChromium XNextSeq 2000RNA-seq of coding RNA from single cellsHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17553Protein 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 traffickingbiostudies-arrayexpressSequencing - 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.Sample Collection - Bone marrow mononuclear cells were thawed, washed and resuspended in PBS containing 2% fetal bovine serum to a concentration of ~800-1,000 cells/µl with high viability >95%.Library Construction - After GEM generation, single index libraries were generated using the 10x Genomics GEM-X Universal 3′ Gene Expression v4, according to manufacturer’s instructions (PN 1000121, 10X Genomics, Pleasanton, CA). Size distribution and concentration of cDNA and final libraries were verified on an TapeStation (Agilent Technologies, Santa Clara, CA) and the concentration of the libraries were measured using Qubit Fluorometer (Thermo Fisher Scientific, Waltham, MA) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA).Nucleic Acid Extraction - The single-cell suspension was loaded at a volume to target of around 8000 cells per sample onto a Chromium X (10x Genomics, Pleasanton, CA) for Gel Bead-In-EMulsions “GEM” generation according to manufacturer’s instructions (10X Genomics, Pleasanton, CA).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesRaphael CarapitofalseSingle-cell RNA-seq analysis of bone marrow cells from a RABGGTA-deficient patient and pediatric controlsProtein 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 trafficking2026-08-17T00:00:00Z2026-08-25T22:13:05.824Z2026-08-25T22:12:50.452ZE-MTAB-17553ERP204260EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0004184