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Human Colorectal Cancer: Targeted, Gene Signature Panel

Spatial Gene Expression dataset analyzed using Space Ranger 1.2.0

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10X Genomics obtained fresh frozen Invasive Adenocarcinoma of the large intestine tissue from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols – Tissue Preparation Guide (Demonstrated Protocol CG000240). Tissue sections of 10µm were placed on Visium Gene Expression slides and fixed and stained following Methanol Fixation, H&E Staining & Imaging for Visium Spatial Protocols (CG000160).

The tissue was AJCC/UICC T4aN0M0, Stage Group IIB.

The H&E image was acquired using a Nikon Eclipse Ti2-E microscope with the following settings:

  • Color camera
  • 10X objective
  • Numerical Aperture: 0.45
  • Exposure: 20 ms

The Visium Gene Expression library (T1T2-E8) was prepared as described in the Visium Spatial Reagent Kits User Guide (CG000239 Rev D). Targeted libraries were prepared following the Targeted Gene Expression - Spatial User Guide (CG000377) using the Human Gene Signature Panel (PN-2000285). Targeted sequencing data was processed using Space Ranger.

  • Sequencing instrument: Illumina NovaSeq 6000, flow cell HHW57DSXY (lane 4)
  • Sequencing depth: 16,795 mean reads per cell
  • Sequencing configuration: Paired-end (28 X 90), Dual-Indexed Sequencing. Read 1: 28 cycles (16 bp barcode, 12 bp UMI); i7 index: 10 cycles; i5 index: 10 cycles; Read 2: 90 cycles (transcript).
  • Slide: V10A13-206
  • Area: C1

Key targeted metrics were:

  • Spots detected: 3,138
  • Median targeted genes per spot: 351
  • Median targeted UMI counts per spot: 635
  • Reads mapped confidently to the targeted transcriptome: 88.2%
  • Total targeted genes detected: 1,134

To maintain donor anonymity, sequence data for this sample is not currently available.

This dataset is licensed under the Creative Commons Attribution license.