10x Genomics obtained fresh frozen Invasive Ductal Carcinoma breast tissue from BioIVT. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide Demonstrated Protocol (CG000240 Rev A). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.
The tissue was AJCC/UICC Stage T2N0M0, ER positive, PR negative, Hercep Test 2+.
- Block ID: 1168993F
- Tumor Grade III
- Sex: Female (Age 60s)
- RIN Score: 9.26
The slide was cover-slipped 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 library was prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev A).
- Sequencing instrument: Illumina NovaSeq 600, flow cell H2LJMDSXY (lane 1-3)
- Sequencing Depth: 47,223 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-E5
- Slide: V19B23-014
- Capture Area: A1
Key cell metrics were:
- Spots detected under tissue - 4,898
- Median UMI counts per spot - 9,720
- Median genes per spot - 3,654
To maintain donor anonymity, sequence data for this sample is not currently available.