{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Raphael Carapito"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15443"],"description":["In this study, we report a patient with a novel homozygous variant in HYOU1 (NM_001130991.3:c.1331C>A, p.Pro444His), who was born to related parents and presented with combined immunodeficiency, failure to thrive, and hypoglycemia.  We undertook a multiomics analysis combining transcriptomics, proteomics, and single cell RNA sequencing analyses, demonstrating a drastic reduction in B cell count and hypogranulation of neutrophils in conformity with the findings of immunophenotyping. Additionally, we showed that despite the HYOU1 transcript being expressed and stable, the patient has HYOU1 deficiency at the protein level. Moreover, single cell RNA sequencing of bone marrow revealed that the B cell differentiation process is prematurely arrested at pre-pro B cell stage. The present dataset corresponds to the bulk RNAseq performed on bone marrow, human dermal fibroblasts (HDF) and PBMCs of the patient and healthy controls."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - SMARTer® Stranded Total RNA-Seq Kit v2 (Takara, Otsu, Shiga, Japan)","Sample Collection - For PBMC: Standard venopuncture followed by ficoll extraction of PBMC For BM:  For HDF:Human dermal fibroblast (HDF) isolation of the proband was performed within three days of the skin biopsies. The biopsy was transferred to a sterile petri dish. Dermis and hypodermis were removed and discarded. Epidermis was cut into small pieces and placed in 25 cm2 flasks. Culture media (Dulbecco's Modified Eagle Medium (10566016, Gibco™, Thermo Fisher Scientific, Waltham, MA, USA) (DMEM) supplemented with 10% inactivated foetal bovine serum (FBS), 40 U/ml penicillin, and 50 mg/ml streptomycin was added to cover the surface after 15 minutes. The media was changed after 24 hours. The cells were passed at 80% confluency using trypsinization. Control HDFs were purchased from Promocell (Heidelberg, Germany).","Sequencing - paired-end (2x75bp) on NextSeq500 (Illumina, San Diego, CA)","Nucleic Acid Extraction - RNA was extracted using the RNeasy Mini Kit (74106, Qiagen, Hilden, Germany)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Raphael Carapito"],"additional_accession":[]},"is_claimable":false,"name":"Bulk RNA sequencing analysis of a patient with an immunodeficiency caused by a novel homozygous missense variant in HYOU1","description":"In this study, we report a patient with a novel homozygous variant in HYOU1 (NM_001130991.3:c.1331C>A, p.Pro444His), who was born to related parents and presented with combined immunodeficiency, failure to thrive, and hypoglycemia.  We undertook a multiomics analysis combining transcriptomics, proteomics, and single cell RNA sequencing analyses, demonstrating a drastic reduction in B cell count and hypogranulation of neutrophils in conformity with the findings of immunophenotyping. Additionally, we showed that despite the HYOU1 transcript being expressed and stable, the patient has HYOU1 deficiency at the protein level. Moreover, single cell RNA sequencing of bone marrow revealed that the B cell differentiation process is prematurely arrested at pre-pro B cell stage. The present dataset corresponds to the bulk RNAseq performed on bone marrow, human dermal fibroblasts (HDF) and PBMCs of the patient and healthy controls.","dates":{"release":"2025-08-25T00:00:00Z","modification":"2025-08-04T12:17:10.986Z","creation":"2025-08-04T12:17:10.986Z"},"accession":"E-MTAB-15443","cross_references":{"ENA":["ERP177776"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}