{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yunjie Li"],"organism":["Homo sapiens"],"software":["SAW(v4.1.0)"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16462"],"description":["Spatial transcriptomic data was generated from human fetal cochleae across 10, 14, and 16 post-conceptual weeks (PCW) using the Stereo-seq platform. Fresh-frozen tissues were sectioned at 10 μm thickness and mounted on pre-chilled capture chips of 0.5×0.5 cm or 1×1 cm sizes. The protocol involved on-chip tissue fixation, permeabilization with 0.1% pepsin, and reverse transcription using a Stereo-seq-specific TSO oligonucleotide. First-strand cDNA was amplified for 15 cycles. Sequencing libraries were constructed via Tn5 transposase fragmentation of 20 ng input cDNA, followed by a 13-cycle amplification with platform-specific primers. Final libraries were sequenced on the MGI DNBSEQ-T7 platform, producing paired-end reads of 35 bp (Read1) and 100 bp (Read2) in length. Raw data was processed through the SAW pipeline (v4.1.0), with reads aligned to the GRCh38 human genome using STAR (v2.5.3). The final output is a spatial gene expression matrix where molecules are quantified by unique Molecular Identifiers (MIs) and mapped to precise spatial locations via Coordinate Identifiers (CIDs)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Final libraries were sequenced on the MGI DNBSEQ-T7 platform. Sequencing was performed with a 35 bp (Read 1) and 100 bp (Read 2) paired-end configuration.","Nucleic Acid Extraction - Tissue sections on chips were permeabilized in 0.01 M HCl supplemented with 0.1% pepsin at 37°C for 12 minutes to release RNA.","Sample Collection - Fresh human fetal cochlear samples at 10, 14, and 16 post-conceptual weeks (PCW) were collected.  Tissues were rinsed with PBS, blotted dry, embedded in OCT compound, and flash-frozen in liquid nitrogen.","Library Construction - The released RNA was reverse-transcribed using a Stereo-seq-specific TSO oligonucleotide to generate first-strand cDNA. After tissue removal and Exonuclease I treatment, cDNA was amplified (15 cycles). The amplified product was fragmented using Tn5 transposase and then further amplified (13 cycles) with Stereo-seq library primers to construct the final sequencing library. Library purification was performed using VAHTS™ DNA Clean Beads."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Spatial transcriptomic data were processed using the SAW pipeline (v4.1.0).  Raw sequencing reads were aligned to the GRCh38 human genome using STAR (v2.5.3).  Gene expression matrices were constructed by counting unique molecular identifiers (UMIs)  for each gene at each spatial location (Coordinate Identifier, CID).  Quality control was performed based on reads per spot, genes detected, and UMI counts.  Following initial processing by SAW, further data normalization, filtering, and analysis  were performed using Seurat (v5.0.2), including log-normalization and identification of  spatially variable features."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-T7"],"study_type":["spatial transcriptomics by high-throughput sequencing"],"species":["Homo sapiens"],"pubmed_authors":["Yunjie Li"],"additional_accession":[]},"is_claimable":false,"name":"A Human Fetal Cochlear Cell Atlas Reveals a Regulatory Blueprint for Spatial Patterning- Stereo-seq","description":"Spatial transcriptomic data was generated from human fetal cochleae across 10, 14, and 16 post-conceptual weeks (PCW) using the Stereo-seq platform. Fresh-frozen tissues were sectioned at 10 μm thickness and mounted on pre-chilled capture chips of 0.5×0.5 cm or 1×1 cm sizes. The protocol involved on-chip tissue fixation, permeabilization with 0.1% pepsin, and reverse transcription using a Stereo-seq-specific TSO oligonucleotide. First-strand cDNA was amplified for 15 cycles. Sequencing libraries were constructed via Tn5 transposase fragmentation of 20 ng input cDNA, followed by a 13-cycle amplification with platform-specific primers. Final libraries were sequenced on the MGI DNBSEQ-T7 platform, producing paired-end reads of 35 bp (Read1) and 100 bp (Read2) in length. Raw data was processed through the SAW pipeline (v4.1.0), with reads aligned to the GRCh38 human genome using STAR (v2.5.3). The final output is a spatial gene expression matrix where molecules are quantified by unique Molecular Identifiers (MIs) and mapped to precise spatial locations via Coordinate Identifiers (CIDs).","dates":{"release":"2026-02-02T00:00:00Z","modification":"2026-05-27T10:01:35.11Z","creation":"2025-12-22T17:47:20.049Z"},"accession":"E-MTAB-16462","cross_references":{"ENA":["ERP187045"],"EFO":["EFO_0002944","EFO_0004170","EFO_0030005","EFO_0005518","EFO_0003816","EFO_0004184"]}}