Technology Showcase Fall 2023
Cambridge, MA • Columbia, MO • Detroit, MI • Durham, NC • Palo Alto, CA • Seattle, WA • Washington, D.C.
Spatially resolved sub-cellular transcriptomics (Stereo-seq) and its applications
Featuring Vikrant Kumar Ph.D.
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Publications
Current Publications that feature Stereo-seq Spatial Transcriptomics
Spatiotemporal insight into early pregnancy governed by immune-featured stromal cells. Yang M, Ong J, Meng F, Zhang F, Shen H, Kitt K, Liu T, Tao W, Du P. Cell. 2023 Sep 28;186(20):4271-4288.e24. doi: 10.1016/j.cell.2023.08.020. Epub 2023 Sep 11. PMID: 37699390.
Single-cell spatial transcriptome reveals cell-type organization in the macaque cortex. Chen A, et. al. Cell. 2023 Aug 17;186(17):3726-3743.e24. doi: 10.1016/j.cell.2023.06.009. Epub 2023 Jul 12. PMID: 37442136.
Clonal dynamics and Stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma. Zhao R, et. al. NPJ Precis Oncol. 2023 Aug 26;7(1):80. doi: 10.1038/s41698-023-00430-8. PMID: 37634047; PMCID: PMC10460394.
Partial alignment of multislice spatially resolved transcriptomics data. Liu X, Zeira R, Raphael BJ. Genome Res. 2023 Jul;33(7):1124-1132. doi: 10.1101/gr.277670.123. Epub 2023 Aug 8. PMID: 37553263; PMCID: PMC10538490.
Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration. Wei X, et.al. Science. 2022 Sep 2;377(6610):eabp9444. doi: 10.1126/science.abp9444. Epub 2022 Sep 2. PMID: 36048929.
Chen A, et.al. Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays. Chen A, et.al. Cell. 2022 May 12;185(10):1777-1792.e21. doi: 10.1016/j.cell.2022.04.003. Epub 2022 May 4. PMID: 35512705.
An invasive zone in human liver cancer identified by Stereo-seq promotes hepatocyte-tumor cell crosstalk, local immunosuppression and tumor progression. Wu L, et.al. Cell Res. 2023 Aug;33(8):585-603. doi: 10.1038/s41422-023-00831-1. Epub 2023 Jun 19. PMID: 37337030; PMCID: PMC10397313.
Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST. Long Y, Ang KS, Li M, Chong KLK, Sethi R, Zhong C, Xu H, Ong Z, Sachaphibulkij K, Chen A, Zeng L, Fu H, Wu M, Lim LHK, Liu L, Chen J. Nature Communications. 2023 Mar 1;14(1):1155. doi: 10.1038/s41467-023-36796-3. PMID: 36859400; PMCID: PMC9977836.
Microbiota-mediated shaping of mouse spleen structure and immune function characterized by scRNA-seq and Stereo-seq. Zhang Y, et. al. J Genet Genomics. 2023 Sep;50(9):688-701. doi: 10.1016/j.jgg.2023.04.012. Epub 2023 May 6. PMID: 37156441.
A single-cell transcriptome atlas profiles early organogenesis in human embryos. Xu Y, et. al. Nat Cell Biol. 2023 Apr;25(4):604-615. doi: 10.1038/s41556-023-01108-w. Epub 2023 Mar 16. PMID: 36928764.
Spatial transcriptomics in human biomedical research and clinical application. Hu, W., Zhang, Y., Mei, J. et al. Curr Med 2, 6 (2023). https://doi.org/10.1007/s44194-023-00023-4
VT3D: a visualization toolbox for 3D transcriptomic data. Guo L, et. al. J Genet Genomics. 2023 Sep;50(9):713-719. doi: 10.1016/j.jgg.2023.04.001. Epub 2023 Apr 11. PMID: 37054878.
Implantation underneath the abdominal anterior rectus sheath enables effective and functional engraftment of stem-cell-derived islets. Liang Z, et. al. Nat Metab. 2023 Jan;5(1):29-40. doi: 10.1038/s42255-022-00713-7. Epub 2023 Jan 9. PMID: 36624157.
Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding. Shen R, et. al. Nat Commun. 2022 Dec 10;13(1):7640. doi: 10.1038/s41467-022-35288-0. PMID: 36496406; PMCID: PMC9741613.
STOmics-GenX: CRISPR based approach to improve cell identity specific gene detection from spatially resolved transcriptomics. Currenti J., et. al. BioRxiv. 2022 Dec 08, 2022.doi: https://doi.org/10.1101/2022.12.08.519589
A cellular hierarchy in melanoma uncouples growth and metastasis. Karras P, Bordeu I, Pozniak J, Nowosad A, Pazzi C, Van Raemdonck N, Landeloos E, Van Herck Y, Pedri D, Bervoets G, Makhzami S, Khoo JH, Pavie B, Lamote J, Marin-Bejar O, Dewaele M, Liang H, Zhang X, Hua Y, Wouters J, Browaeys R, Bergers G, Saeys Y, Bosisio F, van den Oord J, Lambrechts D, Rustgi AK, Bechter O, Blanpain C, Simons BD, Rambow F, Marine JC. Nature. 2022 Oct;610(7930):190-198. doi: 10.1038/s41586-022-05242-7. Epub 2022 Sep 21. Erratum in: Nature. 2022 Nov;611(7934):E4. PMID: 36131018; PMCID: PMC10439739.
Single-Nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma. Ou Z, et. al. Adv Sci (Weinh). 2022 Oct;9(29):e2203040. doi: 10.1002/advs.202203040. Epub 2022 Aug 19. PMID: 35986392; PMCID: PMC9561780.
A Cellular Resolution Spatial Transcriptomic Landscape of the Medial Structures in Postnatal Mouse Brain. Cheng M, et.al. Front Cell Dev Biol. 2022 May 17;10:878346. doi: 10.3389/fcell.2022.878346. PMID: 35656552; PMCID: PMC9152126.
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis. Liu C, et.al. Dev Cell. 2022 May 23;57(10):1284-1298.e5. doi: 10.1016/j.devcel.2022.04.009. Epub 2022 May 4. PMID: 35512701.
High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae. Wang M, et.al. Dev Cell. 2022 May 23;57(10):1271-1283.e4. doi: 10.1016/j.devcel.2022.04.006. Epub 2022 May 4. PMID: 35512700.
Spatial Transcriptome Uncovers the Mouse Lung Architectures and Functions. Jiang Y, et.al. Front Genet. 2022 Mar 9;13:858808. doi: 10.3389/fgene.2022.858808. PMID: 35391793; PMCID: PMC8982079.
Plants
transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial Proc Natl Acad Sci U S A. 2023 Sep 19;120(38):e2310163120. doi: 10.1073/pnas.2310163120. Epub 2023 Sep 13. PMID: 37703282; PMCID: PMC10515167.
Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation. Liu Z, Kong X, Long Y, Liu S, Zhang H, Jia J, Cui W, Zhang Z, Song X, Qiu L, Zhai J, Yan Z. Nat Plants. 2023 Apr;9(4):515-524. doi: 10.1038/s41477-023-01387-z. Epub 2023 Apr 13. PMID: 37055554.
Spatial transcriptome analysis on peanut tissues shed light on cell heterogeneity of the peg. Liu Y, et. al. Plant Biotechnol J. 2022 Sep;20(9):1648-1650. doi: 10.1111/pbi.13884. Epub 2022 Jul 23. PMID: 35792883; PMCID: PMC9398287.
The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves. Xia K, et. al. Dev Cell. 2022 May 23;57(10):1299-1310.e4. doi: 10.1016/j.devcel.2022.04.011. Epub 2022 May 4. PMID: 35512702.
