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Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody

Spatial Gene Expression dataset analyzed using Space Ranger 1.2.0

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Invasive ductal carcinoma was obtained from BioIVT: ASTERAND (Westbury, NY). Raw sequencing data (FASTQ and BAM files) are not included. This dataset is published in Nature Biotechnology: Spatial transcriptomics at subspot resolution with BayesSpace.

Tumor Phenotype:

  • Infiltrating ductal carcinoma of the breast
  • RIN – 9.26
  • Tumor Grade – III
  • AJCC/UICC Stage - T2N0M0
  • AJCC/UICC Stage Group – IIA
  • ER – Positive
  • PR – Negative
  • Hercep Test – 2+
  • Menopausal
  • Age at excision – 50+

Samples were stained with antibodies and DAPI as follows:

  • DAPI to stain for nuclei
  • Anti-CD3 (SP7) (Abcam ab16669) with goat-anti rabbit alexa fluor 647
  • Imaged at 20X on Nikon Eclipse Ti2-E, coverslip down

The Visium Spatial Gene Expression libraries were prepared following the Methanol Fixation, Immunofluorescence Staining & Imaging for Visium Spatial Protocols (CG000312 Rev A) and Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev C).

  • Sequencing instrument: Illumina NovaSeq
  • Sequencing depth: 40,795 reads per spot
  • Sequencing configuration: Paired-end (28 X 90)
  • Sequencing coverage: Read 1: 28bp Read 1 (16bp Visium spatial barcode, 12bp UMI), Read 2: 120bp (transcript), 10bp i7 sample barcode and 10bp i5 sample barcode
  • Dual-Index set: SI-TT-A12
  • Slide: SI-TT-A12
  • Area: A2

Key metrics were:

  • Spots detected under tissue: 4,727
  • Median genes per spot: 2,964
  • Median UMI counts per spot: 6,314

This dataset is licensed under the Creative Commons Attribution license.