biostudies-arrayexpressjiacheng fanHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16331Single-nucleus multiomic data was generated from human fetal cochleae across 11, 14, and 16 post-conceptual weeks (PCW) using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression platform. Snap-frozen tissues were minced and lysed in ice-cold Nuclei Lysis Buffer, followed by filtration through a 40 μm strainer and centrifugation. Nuclear integrity was confirmed via trypan blue staining prior to mild permeabilization using 0.1× Lysis Buffer. After quenching and washing, nuclei were resuspended in Diluted Nuclei Buffer and concentration was adjusted to 4,000–8,000 nuclei/μL. Libraries were prepared following the standard 10X Multiome protocol for simultaneous gene expression and chromatin accessibility profiling. Sequencing was performed on the Illumina platform, producing paired-end reads. Raw data were processed through the Cell Ranger ARC pipeline (v2.0.0) with alignment to the GRCh38 human genome. The final output comprises paired gene expression matrices and chromatin accessibility peaks, both linked to the same individual nuclei through shared barcodes.biostudies-arrayexpressLibrary Construction - For snMultiome-seq, libraries were prepared and loaded following the manufacturer's instructions of the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle. Chip J (10x Genomics) was used for droplet generation. For the gene expression library, Dual Index Kit TT Set A (10x Genomics) was employed, while the ATAC library was constructed using Single Index Kit NT Set A (10x Genomics).Sample Collection - In this study, human embryonic cochleae were collected from medically aborted embryos ranging from 10 to 17 PCW. The study protocol was reviewed and approved by the Ethics Committee of the Eye, Ear, Nose and Throat Hospital of Fudan University, China (Approval No.: 2022166). None of the samples utilized in this study exhibited known genetic abnormalities. Fetuses with severe pregnancy-related complications or congenital developmental abnormalities were excluded. Prior to the procedure, informed consent was obtained from all participating pregnant women after comprehensive counseling, authorizing the use of fetal tissue for research purposes. Fetuses with severe pregnancy lesions and abnormal fetal congenital development were excluded. All patient and sample information was numbered and collected anonymously. For fetal cochlear explant culture, temporal bone was disassociated from aborted fetus. The temporal bone was washed with 1.5 µg/mL ampicillin in ice-cold PBS. The cochleae were isolated with sterile forceps under a stereoscopic microscope.Sequencing - The resulting multiome libraries were sequenced on an Illumina NovaSeq 6000 system using a paired-end 150 bp (PE150) configuration.Nucleic Acid Extraction - Single-nucleus RNA and ATAC sequencing (snMultiome) was performed on cochlear tissues from three human fetuses (11, 14, and 16 PCW) using the 10x Genomics Chromium Multiome platform. Nuclei were isolated by mincing snap-frozen samples in ice-cold lysis buffer, followed by filtration, centrifugation, and mild permeabilization. After quality assessment via trypan blue staining, intact nuclei were resuspended in dilution buffer, quantified, and adjusted to 4,000–8,000 nuclei/μL for subsequent library preparation and sequencing.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - snRNA-seq: Normalized via SCTransform using negative binomial regression to remove technical variations. snATAC-seq: Applied TF-IDF normalization to the peak-count matrix, followed by Latent Semantic Indexing (LSI). Batch effects across samples were corrected using Seurat's integration on principal components and LSI components.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000single nucleus RNA sequencingHomo sapiensjiacheng fanfalseA Human Fetal Cochlear Cell Atlas Reveals a Regulatory Blueprint for Spatial Patterning - sn-MultiomeSingle-nucleus multiomic data was generated from human fetal cochleae across 11, 14, and 16 post-conceptual weeks (PCW) using the 10X Genomics Chromium Next GEM Single Cell Multiome ATAC+ Gene Expression platform. Snap-frozen tissues were minced and lysed in ice-cold Nuclei Lysis Buffer, followed by filtration through a 40 μm strainer and centrifugation. Nuclear integrity was confirmed via trypan blue staining prior to mild permeabilization using 0.1× Lysis Buffer. After quenching and washing, nuclei were resuspended in Diluted Nuclei Buffer and concentration was adjusted to 4,000–8,000 nuclei/μL. Libraries were prepared following the standard 10X Multiome protocol for simultaneous gene expression and chromatin accessibility profiling. Sequencing was performed on the Illumina platform, producing paired-end reads. Raw data were processed through the Cell Ranger ARC pipeline (v2.0.0) with alignment to the GRCh38 human genome. The final output comprises paired gene expression matrices and chromatin accessibility peaks, both linked to the same individual nuclei through shared barcodes.2026-02-04T00:00:00Z2026-05-27T14:40:22.976Z2025-12-03T18:07:27.147ZE-MTAB-16331ERP189357EFO_0002944EFO_0004170EFO_0009809EFO_0005518EFO_0003816EFO_0004184