| Article | DOI | Year | Platform | Species | Tissue | Link |
|---|---|---|---|---|---|---|
| The spatial transcriptomic landscape of the healing intestine following damage | 10.1038/s41467-022-28497-0 | 2022 | Visium | Mouse | intestine | GSE169749; |
| The spatial RNA integrity number assay for in situ evaluation of transcriptome quality | 10-1038-s42003-020-01573-1 | 2021 | Spatial Transcriptomics v1.0 and v2.0 | Human | breast cancer; pediatric brain tumor | https://doi.org/10.17632/kzfd6mbnxg.1 |
| Super-resolved spatial transcriptomics by deep data fusion | 10.1038/s41587-021-01075-3 | 2021 | Spatial Transcriptomics v1.0 and v2.0; Visium | Mouse; Human | MOB; breast cancer; squamous cell carcinoma; small intestine | https://data.mendeley.com/datasets/v8s9nz948s/1; https://data.mendeley.com/datasets/2bh5fchcv6/1 |
| Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin | 10.1016/j.cmet.2021.07.018 | 2021 | Visium | Human | white adipose tissue (s.c) | https://data.mendeley.com/datasets/3bs5f8mvbs/1 |
| Genome-wide spatial expression profiling in formalin-fixed tissues | 10.1016/j.xgen.2021.100065 | 2021 | Visium | Mouse; Human | brain; gynecological carcinosarcoma; soft tissue sarcoma; colon xenograft; lung and kidney organoids; SARS-CoV-2 infected lung biopsy | GSE185715; https://data.mendeley.com/datasets/xjtv62ncwr/1 |
| Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions | 10.1038/s41467-021-26271-2 | 2021 | Spatial Transcriptomics v1.0 | Human | breast cancer (HER2+) | https://zenodo.org/record/4751624. Raw sequencing data: European Genome-Phenome Archive (EGA) ID EGAD00001008031; contact for access: Åke Borg ([email protected]) |
| Integrating spatial gene expression and breast tumour morphology via deep learning | 10.1038/s41551-020-0578-x | 2020 | Spatial Transcriptomics v1.0 | Human | breast cancer | https://data.mendeley.com/datasets/29ntw7sh4r |
| Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma | 10.1016/j.cell.2020.05.039 | 2020 | Spatial Transcriptomics v2.0; Visium | Human | squamous cell carcinoma | GSE144240 |
| Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics | 10.1038/s41598-019-55441-y | 2019 | Spatial Transcriptomics v1.0 | Human | arthritic joint | https://www.spatialresearch.org/resources-published-datasets/doi-10-1038-s41598-019-55441-y/ |
| A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart | 10.1016/j.cell.2019.11.025 | 2019 | Spatial Transcriptomics v1.0 | Human | heart | https://data.mendeley.com/datasets/mbvhhf8m62/2 ; https://data.mendeley.com/datasets/dgnysc3zn5/1 |
| Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis | 10.1126/science.aav9776 | 2019 | Spatial Transcriptomics v1.0 | Mouse; Human | spinal cord (post mortem) | http://als-st.nygenome.org/ ; GSE120374 |
| Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity | 10.1038/s41467-018-04724-5 | 2018 | Spatial Transcriptomics v1.0 | Human | prostate | https://spatialtranscriptomics3d.shinyapps.io/STProstateResearch/ ; https://www.spatialresearch.org/resources-published-datasets/10-1038-s41467-018-04724-5/ |
| Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma | 10.1158/0008-5472.CAN-18-0747 | 2018 | Spatial Transcriptomics v1.0 | Human | cutaneous malignant melanoma | https://www.spatialresearch.org/resources-published-datasets/doi-10-1158-0008-5472-can-18-0747/ |
| Spatially resolved transcriptome profiling in model plant species | 10.1038/nplants.2017.61 | 2017 | Spatial Transcriptomics v1.0 | Arabidopsis thaliana; Picea abies; Populus tremula | https://www.spatialresearch.org/resources-published-datasets/10-1038-nplants-2017-61/ | |
| Spatial detection of fetal marker genes expressed at low level in adult human heart tissue | 10.1038/s41598-017-13462-5 | 2017 | Spatial Transcriptomics v1.0 | Human | heart | https://www.spatialresearch.org/resources-published-datasets/doi10-1038s41598-017-13462-5/ |
| Visualization and analysis of gene expression in tissue sections by spatial transcriptomics | 10.1126/science.aaf2403 | 2016 | Spatial Transcriptomics v1.0 | Mouse; Human | MOB; Breast cancer | https://www.spatialresearch.org/resources-published-datasets/doi-10-1126science-aaf2403/ |
| Massive and parallel expression profiling using microarrayed single-cell sequencing | 10.1038/ncomms13182 | 2016 | MASC-seq | Human | CLL; MCF-7 | https://www.spatialresearch.org/resources-published-datasets/doi10-1038ncomms13182/ |
Datasets from our published articles can be found under the following links:
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics (2016)
DOI: 10.1126/science.aaf2403
Massive and parallel expression profiling using microarrayed single-cell sequencing (2016)
DOI: 10.1038/ncomms13182
Spatially resolved transcriptome profiling in model plant species (2017)
DOI: 10.1038/nplants.2017.61
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue (2017)
DOI: 10.1038/s41598-017-13462-5
ST Spot Detector: a web-based application for automatic spot and tissue detection for Spatial Transcriptomics image data sets (2018)
DOI: 10.1093/bioinformatics/bty030
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity (2018)
DOI: 10.1038/s41467-018-04724-5
Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma (Thrane K. et al., 2018)
DOI: 10.1158/0008-5472.CAN-18-0747
Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics (Carlberg K. et al., 2019)
DOI: 10.1038/s41598-019-55441-y
A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart (Asp M. et al., 2019)
DOI: 10.1016/j.cell.2019.11.025
Integrating spatial gene expression and breast tumour morphology via deep learning (He B. et al., 2020)
DOI: 10.1038/s41551-020-0578-x
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality (Kvastad L. et al., 2021)
DOI: 10-1038-s42003-020-01573-1