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Human Intestine Cancer (FPPE)

Spatial Gene Expression dataset analyzed using Space Ranger 1.3.0

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5 µm section from Human Intestinal Cancer. FFPE tissue purchased from BioIVT Asterand Human Tissue Specimens.

  • Block 1281585B
  • Large Intestine Colorectal cancer
  • Brightfield camera, Magnification: 20x

Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).

  • Sequencing instrument: Illumina NovaSeq 6000, flow cell HCCVHDSX2 (lanes 1-2)
  • Sequencing depth: 77,288 reads per spot
  • Sequencing configuration: 28 bp read 1 (16 bp Visium spatial barcode, 12 bp UMI), 50 bp read 2 (transcript), 10 bp i7 sample barcode and 10 bp i5 sample barcode
  • Dual-Index set: SI-TS-B1
  • Slide: V10L13-021
  • Area: B1

Key metrics were:

  • Spots detected under tissue: 2,660
  • Median genes per spot: 7,438
  • Median UMI counts per spot: 25,312

This dataset is licensed under the Creative Commons Attribution license.