Human Breast Cancer: Targeted, Immunology Panel

10X Genomics obtained fresh frozen human Invasive Lobular 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 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 Stage Group I, ER positive, PR positive, HER2 negative.

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-A6) 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 Immunology Panel (PN-2000286). Targeted sequencing data was processed using Space Ranger.

• Sequencing instrument: Illumina NovaSeq 6000, flow cell HHWHLDSXY (lane 4)
• Sequencing depth: 16,141 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: V19L29-095
• Area: A1

Key targeted metrics were:

• Spots detected: 4,325
• Median targeted genes per spot: 203
• Median targeted UMI counts per spot: 672
• Reads mapped confidently to the targeted transcriptome: 84.2%
• Total targeted genes detected: 973

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

This dataset is licensed under the Creative Commons Attribution license.