Human Breast Cancer (Block A Section 2)
Spatial Gene Expression dataset analyzed using Space Ranger 1.0.0
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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: 137,262 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-H10
- Slide: V19L29-098
- Area: B1
Key cell metrics were:
- Spots detected under tissue - 4,015
- Median UMI counts per spot - 16,502
- Median genes per spot - 5,100
To maintain donor anonymity, sequence data for this sample is not currently available.
This dataset is licensed under the Creative Commons Attribution license.