Human Breast Cancer: Whole Transcriptome Analysis

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). Sequencing data was processed using Space Ranger.

• Sequencing instrument: Illumina NovaSeq 6000, flow cell HHYWHDSXY (lanes 1-4)
• Sequencing depth: 72,436 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 metrics were:

• Spots detected: 4,325
• Median genes per spot: 3,671
• Median UMI counts per spot: 9,465

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

This dataset is licensed under the Creative Commons Attribution license.