Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 Platforms for Single-Cell Spatial Transcriptomics of Murine Organs(Dataset ID: STDS0000385)

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Dataset information
Summary:
We compared the performance of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms for spatial transcriptomic analysis using SeekSpace technology. Six samples from murine brain (n=5) and lung (n=1) tissues were used. Spatial transcriptomics libraries were constructed following the SeekSpace protocol and sequenced on both platforms using paired-end 150 bp reads. The same cDNA libraries were sequenced to ensure comparability. SURFSeq 5000 uses self-developed SURF sequencing chemistry and high-resolution optics, while NovaSeq 6000 employs Illumina's SBS chemistry. Sequencing data from both platforms were processed using the same bioinformatics pipeline to evaluate performance in spatial transcriptomics applications.
Overall design:
Spatial transcriptomics was performed on brain (n=5) and lung (n=1) tissues from normal C57BL/6J male mice (6–8 weeks old). Libraries were prepared using the SeekSpace protocol and sequenced on both Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 platforms with paired-end 150 bp reads. Identical cDNA libraries were used for both platforms. Data were analyzed using the same bioinformatics pipeline to compare sequencing performance.
Platform:
Gene Mind -SURFSeq 5000 | Illumina-NovaSeq 6000
Tissues:
Brain | Lung
Submission date: 2025-05-20Update date: 2025-05-20
Sample number: 12Section number: 12
DOI: To be continue
Contributors
WANG Qianwen
Accessions
No results.
How to cite
  • Cite database of STOmicsDB:
    [1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
  • Cite visualization dataset:
    [2] WANG Qianwen. Comparison of Illumina NovaSeq 6000 and GeneMind SURFSeq 5000 Platforms for Single-Cell Spatial Transcriptomics of Murine Organs[DS/OL]. STOmicsDB, 2025[2025-05-20]. https://db.cngb.org/stomics/datasets/STDS0000385/. doi: xxxxxx
    #Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
  • Cite original data article:
    No results.