Full description
Raw sequencing data (fastq and BAM files) of stage III and IV HNSCC samples.
Fresh tumour tissues were snap-frozen in isopentane, embedded in OCT, cryosectioned, and mounted on 10x Genomics Visium slides. After H&E staining and imaging, permeabilisation times were optimised using fluorescent cDNA tissue prints. Sections were then fixed, permeabilised, and reverse-transcribed to generate spatially barcoded cDNA, which was amplified, fragmented, and indexed for library construction. Final libraries, incorporating P5/P7 adaptors and sample-specific i7 indices, were sequenced on Illumina platforms, with Read 1 capturing spatial barcodes and UMIs and Read 2 sequencing cDNA inserts.
Image alignment, read mapping, and quantification were performed with Space Ranger. Tissue and fiducial spots were detected and aligned to generate spatial coordinates. Sequencing reads were mapped to the reference genome using STAR, classified as exonic, intronic, or intergenic, and uniquely mapped exonic reads were retained. Unique molecular identifiers (UMIs) were error-corrected by collapsing single-base mismatches and discarding ambiguous assignments. Only confidently mapped and corrected UMIs were used for final gene expression quantification across spatially resolved tissue sections.
Issued: 2025
Created:
Spatial Coverage And Location
text: Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).
Subjects
Biological Sciences |
Biomedical and Clinical Sciences |
Biochemistry and Cell Biology |
Bioinformatics and Computational Biology |
Cancer Cell Biology |
Cell Development, Proliferation and Death |
Collagen |
Ctag2 |
Head and neck squamous cell carcinoma |
Oncology and Carcinogenesis |
Sequence Analysis |
Single-cell transcriptomics |
Spatial transcriptomics |
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Identifiers
- usc : 11294350360002621
