There is a newer version of the record available.

Published March 14, 2025 | Version v3
Dataset Open

Datasets collected for benchmarking in spatial transcriptomics

Authors/Creators

Description

Datasets collected for benchmarking in spatial transcriptomics. In addition, the code for benchmarking (March 2025 version) is also located here and can be accessed on the GitHub website https://github.com/XiDsLab/svg-benchmark.

Files

svg-benchmark-main.zip

Files (92.2 MB)

Name Size Download all
md5:197a5de438cae8ff16db577064a9c5ad
92.2 MB Preview Download

Additional details

Software

Repository URL
https://github.com/XiDsLab/svg-benchmark

References

  • Chen, A., et al., Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Cell, 2022. 185(10): p. 1777-1792. e21.
  • Maynard, K.R., et al., Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience, 2021. 24(3): p. 425-436.
  • Ortiz, C., et al., Molecular atlas of the adult mouse brain. Science Advances, 2020. 6(26): p. eabb3446.
  • Moncada, R., et al., Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas. Nature Biotechnology, 2020. 38(3): p. 333-342.
  • Wang, X., et al., Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science, 2018. 361(6400): p. eaat5691.
  • Srivatsan, S.R., et al., Embryo-scale, single-cell spatial transcriptomics. Science, 2021. 373(6550): p. 111-117.
  • Eng, C.-H.L., et al., Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+. Nature, 2019. 568(7751): p. 235-239.
  • Human Breast Cancer: Ductal Carcinoma In Situ, Invasive Carcinoma (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2021.
  • Human Cervical Cancer (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2022.
  • Human Intestine Cancer (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2022.
  • Normal Human Prostate (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2021.
  • Adult Mouse Brain (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2021.
  • Adult Mouse Kidney (FFPE), Spatial Gene Expression Dataset by Space Ranger 1.3.0. 10x Genomics, 2021.
  • Adult Mouse Brain Coronal Section (Fresh Frozen), Spatial Gene Expression Dataset by Space Ranger 2.1.0. 10x Genomics, 2023.
  • Human Heart, Spatial Gene Expression Dataset by Space Ranger 1.1.0. 10x Genomics, 2020.
  • Mouse Brain Serial Section 2 (Sagittal-Anterior), Spatial Gene Expression Dataset by Space Ranger 1.1.0. 10x Genomics, 2020.
  • Mouse Brain Serial Section 1 (Sagittal-Posterior), Spatial Gene Expression Dataset by Space Ranger 1.1.0. 10x Genomics, 2020.
  • Mouse Kidney Section (Coronal), Spatial Gene Expression Dataset by Space Ranger 1.1.0. 10x Genomics, 2020.
  • Adult Mouse Olfactory Bulb, Spatial Gene Expression Dataset by Space Ranger 2.0.0. 10x Genomics, 2022.
  • Andersson, A., et al., Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions. Nature Communications, 2021. 12(1): p. 6012.
  • Cho, C.-S., et al., Microscopic examination of spatial transcriptome using Seq-Scope. Cell, 2021. 184(13): p. 3559-3572. e22.
  • Liu, Y., et al., High-spatial-resolution multi-omics sequencing via deterministic barcoding in tissue. Cell, 2020. 183(6): p. 1665-1681. e18.
  • Vickovic, S., et al., High-definition spatial transcriptomics for in situ tissue profiling. Nature Methods, 2019. 16(10): p. 987-990.
  • Rodriques, S.G., et al., Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution. Science, 2019. 363(6434): p. 1463-1467.
  • Cable, D.M., et al., Robust decomposition of cell type mixtures in spatial transcriptomics. Nature Biotechnology, 2022. 40(4): p. 517-526.