{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Roser Vilarrasa-Blasi"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-17252"],"description":["These samples are part of a study aimed at understanding B lymphopoiesis in the human bone marrow throughout the lifespan and guiding in vitro B lymphopoiesis. This dataset contains transcriptomic data from prenatal and adult bone marrow samples, as well as in vitro experiments, together with the corresponding raw data from prenatal bone marrow and in vitro samples. For a subset of samples, cell-hashing oligo (HTO) data used for sample demultiplexing are also included."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Libraries were sequenced on a Novaseq 6000 system to a minimum coverage of 50,000 raw reads per cell, using the sequencing format: Read 1, 28 cycles; i7 index: 10 cycles, i5 index: 10 cycles; Read 2, 90 cycles. For the cell hashing workflow, Chromium Next GEM Single Cell 5′ v2 with Feature Barcoding technology for Cell Surface Protein was used (5’ Feature Barcode kit). Feature Barcode were sequenced to a target depth of 5,000 reads per cell.","Nucleic Acid Extraction - Adherent material was removed from the fetal bone marrow samples, and the ends of the bones were cut. Bone marrow cells were recovered by flushing from one end of the bone. Cells were filtered through a 70µm strainer and centrifuged at 500xg for 5 minutes. After centrifugation, red blood cells were lysed using RBC lysis buffer according to manufacturer’s instructions (eBioscience #00-4300), and washed with wash buffer containing PBS (Gibco #20012027), 0.5% BSA (Miltenyi #130-091-376) and 2mM EDTA (Life Technologies #AM9260G) to reduce clumping24. Cells were then counted and processed in one or more of the following way: (1) sequencing the whole population; (2) enrichment of CD34-positive cells using the CD34-positive selection kit (Miltenyi Biotec #130-046-702), a","Sample Collection - The human embryonic and fetal material was provided by the Joint MRC / Wellcome Trust (Grant #MR/006237/1) Human Developmental Biology Resource (http://www.hdbr.org) following elective of pregnancy, with written informed consent and approved by the London - Fulham Research Ethics Committee (REC reference 23/LO/0312). HDBR is regulated by the UK Human Tissue Authority (HTA; https://www.hta.gov.uk) and operates in accordance with the relevant HTA Codes of Practice.","Library Construction - Library preparation was carried out according to the manufacturer’s protocol for the Chromium Next GEM Single Cell 5’ v2 (DUAL) Kit (10x Genomics)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Generated transcriptomic libraries and external datasets were aligned to the GRCh38 reference genome (v.3.0.0), followed by cell calling, transcript quantification and QC using the Cell Ranger Software (v.3.0.2; 10x Genomics) with default parameters."],"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":["Luz Garcia-Alonso","Roser Vilarrasa-Blasi","Roser Vento-Tormo"],"additional_accession":[]},"is_claimable":false,"name":"Multi-omics analysis of human bone marrow across fetal and adult stages informs strategies for in vitro B lymphopoiesis - scRNA-seq dataset","description":"These samples are part of a study aimed at understanding B lymphopoiesis in the human bone marrow throughout the lifespan and guiding in vitro B lymphopoiesis. This dataset contains transcriptomic data from prenatal and adult bone marrow samples, as well as in vitro experiments, together with the corresponding raw data from prenatal bone marrow and in vitro samples. For a subset of samples, cell-hashing oligo (HTO) data used for sample demultiplexing are also included.","dates":{"release":"2026-09-11T00:00:00Z","modification":"2026-09-11T14:27:39.855Z","creation":"2026-07-01T17:22:03.948Z"},"accession":"E-MTAB-17252","cross_references":{"ENA":["ERP204787"],"EGA":["EGAD00001016347"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}