biostudies-arrayexpressYunjie LiHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16612Human cochlear organoids were derived from human pluripotent stem cell–based differentiation and maintained in CHIR99021-containing proliferative medium (EFI). Organoids were cultured under proliferative conditions for 10 days, after which they were transduced with 3 types of adeno-associated virus (AAV). Following viral transduction, organoids were switched to differentiation conditions and cultured for an additional 7 days. At the designated time point, cochlear organoids were harvested and immediately transferred to ice-cold oxygenated artificial tissue preservation solution. Under microscopic guidance, organoids were gently dissociated to obtain single-cell suspensions. Enzymatic digestion was performed using 0.125% trypsin at 37°C for 20 minutes, followed by gentle mechanical trituration. The resulting cell suspension was filtered through a 40 μm cell strainer and subjected to red blood cell lysis where necessary. Cell viability was assessed using a LUNA-FL automated cell counter with LIVE/DEAD staining, and samples with viability exceeding 80% were processed for downstream analysis. Single-cell RNA-sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.biostudies-arrayexpressLibrary Construction - For scRNA-seq, single-cell suspensions with viability exceeding 80% were used for scRNA-seq library preparation. Libraries were constructed according to the manufacturer's protocol using the Chromium Controller instrument and the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1. Library preparation was carried out according to the manufacturer’s protocol.Sequencing - The resulting libraries were normalized, pooled, and sequenced on an Illumina NovaSeq 6000 system with a 150 bp paired-end configuration.Nucleic Acid Extraction - For scRNA-seq, harvested organoids were dissociated into single-cell suspensions by mincing and trypsin digestion at 37 °C for 20 min. After neutralization and filtration through a 40 μm strainer, cells were treated with RBC lysis buffer, washed, and resuspended in MEM supplemented with 1% BSA and RNase inhibitor. Cell concentration and viability were assessed using a LUNA-FL™ automated cell counter with LIVE/DEAD staining.Sample Collection - Human cochlear organoids were generated from human pluripotent stem cell–based differentiation and served as the biological samples for this study. Organoids were maintained in CHIR99021-containing proliferative medium (EFI) and expanded for 10 days. Subsequently, organoids were subjected to adeno-associated virus (AAV)–mediated gene activation and cultured for an additional 7 days under differentiation conditions prior to sample collection. At the designated collection time point, cochlear organoids were harvested and immediately transferred to ice-cold oxygenated artificial tissue preservation solution.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The resulting libraries were normalized, pooled, and sequenced on an Illumina NovaSeq 6000 system with a 150 bp paired-end configuration.UnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq 6000RNA-seq of coding RNA from single cellsHomo sapiensYunjie LifalseA Human Fetal Cochlear Cell Atlas Reveals a Regulatory Blueprint for Spatial Patterning- scRNA-seq-2Human cochlear organoids were derived from human pluripotent stem cell–based differentiation and maintained in CHIR99021-containing proliferative medium (EFI). Organoids were cultured under proliferative conditions for 10 days, after which they were transduced with 3 types of adeno-associated virus (AAV). Following viral transduction, organoids were switched to differentiation conditions and cultured for an additional 7 days. At the designated time point, cochlear organoids were harvested and immediately transferred to ice-cold oxygenated artificial tissue preservation solution. Under microscopic guidance, organoids were gently dissociated to obtain single-cell suspensions. Enzymatic digestion was performed using 0.125% trypsin at 37°C for 20 minutes, followed by gentle mechanical trituration. The resulting cell suspension was filtered through a 40 μm cell strainer and subjected to red blood cell lysis where necessary. Cell viability was assessed using a LUNA-FL automated cell counter with LIVE/DEAD staining, and samples with viability exceeding 80% were processed for downstream analysis. Single-cell RNA-sequencing libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s instructions. Libraries were sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads.2026-02-11T00:00:00Z2026-05-27T13:38:32.358Z2026-02-11T10:47:10.393ZE-MTAB-16612ERP188985EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184