Spatial Transcriptomic and Single-Cell Atlas of Stage-III and Stage-IV Head and Neck Squamous Cell Carcinoma (HNSCC)

Guoying Ni; Binhong  Chen; Yuandong Luo; Quanlan Fu; Junjie Li; Hejie Li; Ian H Frazer; Xiao Song Liu; Jingjia  Li; Tianfang Wang

doi:10.25907/00970

Dataset

Spatial Transcriptomic and Single-Cell Atlas of Stage-III and Stage-IV Head and Neck Squamous Cell Carcinoma (HNSCC)

Guoying Ni, Binhong Chen, Yuandong Luo, Quanlan Fu, Junjie Li, Hejie Li, Ian H Frazer, Xiao Song Liu, Jingjia Li and Tianfang Wang

University of the Sunshine Coast

2025

DOI:

https://doi.org/10.25907/00970

Appears in UniSC Research Data Collection

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Abstract

Cell development, proliferation and death

Sequence analysis

Cancer cell biology

Spatial transcriptomics

Head and neck squamous cell carcinoma

Single-cell transcriptomics

Collagen

Ctag2

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.

Details

Title: Spatial Transcriptomic and Single-Cell Atlas of Stage-III and Stage-IV Head and Neck Squamous Cell Carcinoma (HNSCC)
Authors: Guoying Ni (Data Collector) - First People's Hospital of Foshan
Binhong Chen (Data Collector) - First People's Hospital of Foshan
Yuandong Luo - Zhongao Biomedical Technology (China)
Quanlan Fu (Data Collector) - Zhongao Biomedical Technology (China)
Junjie Li (Data Collector) - Zhongao Biomedical Technology (China)
Hejie Li (Data Collector) - University of the Sunshine Coast
Ian H Frazer (Data Collector) - The University of Queensland
Xiao Song Liu (Data Collector) - First People's Hospital of Foshan
Jingjia Li (Data Collector) - First People's Hospital of Foshan
Tianfang Wang (Data Collector) - University of the Sunshine Coast
Format: .fastq; 360 GB
Location: Gene Denovo Biotechnology Co., Ltd (Guangzhou, China).
Publisher: University of the Sunshine Coast
Date collected: Oct-2023–Apr-2024
Date published: 2025
DOI: 10.25907/00970
Organisation Unit: School of Science and Engineering - Legacy; GeneCology Research Centre - Legacy; School of Science, Technology and Engineering
Language: English
Record Identifier: 991171944302621
Output Type: Dataset

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