Published March 14, 2025 | Version v4
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, svg-benchmark-main.zip) is also located here and can be accessed on the GitHub website https://github.com/XiDsLab/svg-benchmark.

Files

10X_DLPFC.zip

Files (11.0 GB)

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md5:203a11a8bdb7c4c40ad0abce1c64a89a
4.4 GB Preview Download
md5:07417863d8377c28dd3fe8cfa9899aa3
130.3 MB Preview Download
md5:2fe73f97110806e8916f5daa2c957a87
130.4 MB Preview Download
md5:9ce8fe126ca3645ede5eadba3d401975
97.0 MB Preview Download
md5:286033565d7d1c053d5665b62ffda4ca
379.5 MB Preview Download
md5:4b940f96edc0b9f33e4239104420bf61
326.6 MB Preview Download
md5:79e9229fe4345623fd60a4ab9084e110
281.5 MB Preview Download
md5:272806cb6b15a718f2b135965637a182
214.6 MB Preview Download
md5:771d757e55c19b595dab90545ca6e7f6
115.4 MB Preview Download
md5:7f35c4a03c540bdeec1b8c5cbcede858
246.2 MB Preview Download
md5:8399c586e4ff063d40c3fac373e4e73b
338.6 MB Preview Download
md5:7d3152a49cf946769bb1eac879996e57
271.0 MB Preview Download
md5:3b50ab298a2c2ceaa791c25c2af76df0
285.1 MB Preview Download
md5:6540e0e7c421ae8438a8802c064754e5
13.1 MB Preview Download
md5:b0489bddd62a8017343c923b3069e94b
19.8 MB Preview Download
md5:4f7037165309f6a54c68aadbf9678102
404.1 MB Preview Download
md5:420feb015e579690984b87da0447d12a
454.4 MB Preview Download
md5:4d49046888fcdfa09370416d5511fe62
3.5 MB Preview Download
md5:790809c069c9f5f205892d96c56a7a1a
49.2 MB Preview Download
md5:a8a9e933525a695de2208d1a1c29e83f
28.0 MB Preview Download
md5:551fe85a7b07103bb3e74a169d4c8aa2
1.9 GB Preview Download
md5:830f6c5e37ff67fe3d3be1ab7ce46efb
8.6 MB Preview Download
md5:a3c584e60177993dbd5128e717225609
20.2 MB Preview Download
md5:14ffeb235ae9543de90eb8a526f50fae
11.8 MB Preview Download
md5:089cb97efeea91e11ee92a9a2a947bd5
32.3 MB Preview Download
md5:994dd75063751ab49ae0796bec76761c
86.2 MB Preview Download
md5:de5499e8cddd8918e41e72c702e1337f
91.2 MB Preview Download
md5:e71528c1eb525d6d9ece37a81567061d
99.1 MB Preview Download
md5:89e2b350e71a59f7467b4fd70d71aa82
350.3 MB Preview Download
md5:87f2f522356a175da12079b04ac93877
594.0 kB Preview Download
md5:0e787a264b543bc27a2dc6dc0c09296d
93.2 MB Preview Download
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.