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 4.0 International (CC BY 4.0) license. 10x citation guidelines available here.