biostudies-arrayexpressKazumasa KanemaruHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-17440This experiment uses 10x Genomics Visium HD spatial transcriptomics to characterise the cellular and molecular organisation of the developing human heart.biostudies-arrayexpressSample Collection - Human fetal heart tissue was collected with appropriate informed consent and ethical approval. Tissue was fixed in formalin, processed into formalin-fixed paraffin-embedded (FFPE) blocks, sectioned, and mounted onto Visium HD Spatial Gene Expression slides according to the 10x Genomics tissue preparation guidelines.Nucleic Acid Extraction - No separate nucleic acid extraction was performed. RNA transcripts were detected directly within FFPE tissue sections using the Visium HD probe-based workflow. Gene-specific probe pairs were hybridised to target RNA molecules in situ and ligated before spatial capture and library preparation.Library Construction - Spatial gene-expression libraries were prepared using the 10x Genomics Visium HD Spatial Gene Expression probe-based workflow according to the manufacturer’s instructions. FFPE tissue sections were deparaffinised, stained and imaged before probe hybridisation. Gene-specific probe pairs were hybridised to target transcripts and ligated. The ligated probe products were released and captured on the Visium HD slide, where spatial barcodes and unique molecular identifiers were incorporated. Libraries were amplified, indexed and purified according to the 10x Genomics protocol. No ERCC or other RNA spike-in controls were added.Sequencing - Libraries were sequenced using paired-end, dual-indexed Illumina sequencing. Read 1 contained the unique molecular identifier and spatial barcode and was sequenced for 43 cycles. The i7 and i5 sample indexes were each sequenced for 10 cycles. Read 2 contained the ligated probe insert and was sequenced for 50 cycles. Read 2 therefore represented the probe-derived insert rather than transcript-derived cDNA.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - No normalization or data transformation was performed. Only raw sequencing data are included in this submission.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsHistocore Arcadia H (Leica Biosystems); Microtome RM2255 (Leica Biosystems)Not applicableIllumina NovaSeq XN.A.10x Genomics CytAssistspatial transcriptomics by high-throughput sequencingHomo sapiensSarah A. TeichmannKrzysztof PolanskiKazumasa KanemarufalseSpatial transcriptomics of human heart developmentThis experiment uses 10x Genomics Visium HD spatial transcriptomics to characterise the cellular and molecular organisation of the developing human heart.2026-09-23T00:00:00Z2026-09-23T12:17:24.609Z2026-08-03T13:52:02.983ZE-MTAB-17440ERP203235EFO_0002944EFO_0004170EFO_0030005EFO_0005518EFO_0003816EFO_0004184