Mouse Tissue Microarray in 3x3 Layout with 2 mm Edge to Edge Spacing (FFPE)
Spatial Gene Expression dataset analyzed using Space Ranger 2.0.1
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This dataset is used for the Analyzing CytAssist Tissue Microarray Data with spaceranger count tutorial. The FASTQ and image inputs along with individual manual alignment file for each core, and the aggregation CSV are provided. The datasets include outputs from the spaceranger count runs for all tissue cores as well as at individual tissue core level.
10x Genomics obtained FFPE mouse lung and brain tissue blocks from Charles River Laboratories to prepare the tissue microarray (TMA) block. The TMA cores of 2 mm diameter were laid out in a 3x3 grid layout with 2 mm edge to edge spacing. The TMA block was sectioned as described in Visium CytAssist Spatial Gene Expression for FFPE – Tissue Preparation Guide Demonstrated Protocol (CG000518). Tissue section of 5 µm was placed on a standard glass slide, and H&E-stained following deparaffinization. Sections were coverslipped with 85% glycerol, imaged by color camera, decoverslipped, followed by destaining & decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression slide with 11 mm Capture Area. The probe extension and library construction steps follow the standard Visium for FFPE workflow outside of the instrument.
The TMA layout on the Visium CytAssist Spatial Gene Expression slide with 11 mm Capture Area.
The H&E image was acquired using Olympus VS200 Slide Scanning Microscope with these settings:
- Olympus objective magnification: 20x UPLXAPO Objective
- Numerical Aperture: 0.8
- Camera: iDS (VS-264C) color camera with 3.45 um pixel size
Libraries were prepared following the Visium CytAssist Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000495).
- Sequencing instrument: Illumina Novaseq
- Sequencing depth: 613,990,414 reads / 82.7% sequencing saturation
- Sequencing configuration: 28 bp read 1 (16 bp Visium spatial barcode, 12 bp UMI), 90 bp read 2 (transcript), 10 bp i7 sample barcode and 10 bp i5 sample barcode
- Dual-Index set: I-TS-C1
- Slide: V52Y10-293
- Area: A1
Loupe Browser 6.4.1 was used to generate the manual alignment file that contains information about both the CytAssist Image Alignment and Fiducial Alignment for each of the individual tissue core.
This dataset is licensed under the Creative Commons Attribution license.