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Human Lymph Node

Spatial Gene Expression dataset analyzed using Space Ranger 1.0.0

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10x Genomics obtained fresh frozen human lymph node from BioIVT Asterand. The tissue was embedded and cryosectioned as described in Visium Spatial Protocols - Tissue Preparation Guide Demonstrated Protocol (CG000240). Tissue sections of 10 µm thickness were placed on Visium Gene Expression Slides.

The H&E image was acquired using a Nikon Ti2-E microscope with the following settings:

  • Color camera
  • 10X objective
  • Numerical Aperture: 0.45
  • Exposure: 2 ms
  • Gain: 4.5X

The Visium Spatial Gene Expression library was prepared following the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239).

  • Sequencing instrument: Illumina NovaSeq 6000
  • Sequencing Depth: 123,189 reads per spot
  • Sequencing Configuration: 28 x 120 bp
  • Sequencing Coverage: Read 1 - 16 bp (includes 16 bp Spatial Barcode, 12 bp UMI); Read 2 - 120 bp (transcript); i7 sample index - 10 bp; i5 sample index - 10 bp.
  • Dual-Index set: T1T2-E3
  • Slide: V19L01-033
  • Area: A1

Key cell metrics were:

  • Spots detected under tissue - 4,039
  • Median UMI counts per spot - 16,853
  • Median genes per spot - 5,347

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

This dataset is licensed under the Creative Commons Attribution license.