{"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-17242"],"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 chromatin accessibility and paired gene expression from prenatal bone marrow samples, together with the corresponding raw data."],"repository":["biostudies-arrayexpress"],"sample_protocol":["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","Library Construction - Library preparation was carried out according to the manufacturer’s protocol for Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (10x Genomics).","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.","Sequencing - Libraries were sequencing, aiming at a minimum coverage of 50,000 raw reads per nuclei on the Novaseq 6000 systems, using the sequencing format ATAC from multiome: read 1: 50 cycles; i7 index: 8 cycles, i5 index: 24 cycles, read 2: 49 cycles. Gene expression libraries generated from the Multiome assay were sequenced using the same configuration as the scRNA-seq libraries."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Single-cell ATAC-seq fragment files generated by CellRanger-arc (v.2.0.1) for 10x multiome libraries or CellRanger-atac (v2.1.0) for scATAC-seq libraries were imported into ArchR123 (v1.0.2). Low-quality droplets (transcription start site enrichment score  <4 or number of fragments <1,000) and predicted doublets were removed. Dimensionality reduction was performed using Latent Semantic Indexing, followed by UMAP visualization and clustering. Pseudo-bulk replicates were generated for each cluster, and 501-bp fixed-width peaks were called using MACS2 (v2.2.7.1)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["single nucleus RNA sequencing"],"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 - Multiome 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 chromatin accessibility and paired gene expression from prenatal bone marrow samples, together with the corresponding raw data.","dates":{"release":"2026-09-11T00:00:00Z","modification":"2026-09-11T20:45:28.29Z","creation":"2026-06-22T14:12:48.89Z"},"accession":"E-MTAB-17242","cross_references":{"ENA":["ERP195529"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009809","EFO_0005518","EFO_0003816","EFO_0004184"]}}