All datasets

Human Breast Cancer (Block A Section 1)

Spatial Gene Expression dataset analyzed using Space Ranger 1.1.0

Assess data quality
View summary metrics to assess data quality and more.
View summary
Visualize and explore data
Discover differentially expressed genes, visualize your favorite genes, and explore your data with our visualization software.

Learn about Visium analysis

10x Genomics obtained fresh frozen Invasive Ductal Carcinoma breast 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 10 µm thickness were placed on Visium Gene Expression Slides.

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

  • Color camera
  • 20X objective
  • Numerical Aperture: 0.75
  • Exposure: 10 ms
  • Gain: 4.5X

The tissue was AJCC/UICC Stage Group IIA, ER positive, PR negative, Her2 positive and annotated with:

  • Ductal carcinoma in situ
  • Lobular carcinoma in situ
  • Invasive Carcinoma

The Visium Spatial Gene Expression library was prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239).

  • Sequencing instrument: Illumina NovaSeq 6000
  • Sequencing Depth: 150,392 reads per spot
  • Sequencing Configuration: 28 x 120 bp
  • Sequencing Coverage: Read 1 - 16 bp (includes 16 bp Spatial Barcode, 12 bp UMI); Read 2 - 120 bp (transcript); i7 sample index - 10 bp; i5 sample index - 10 bp.
  • Dual-Index set: T1T2-F10
  • Slide: V19L29-097
  • Area: B1

Key cell metrics were:

  • Spots detected under tissue - 3,798
  • Median UMI counts per spot - 20,762
  • Median genes per spot - 6,026

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

This dataset is licensed under the Creative Commons Attribution license.