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Museum of Spatial Transcriptomics

Moses, Lambda and Pachter, Lior (2021) Museum of Spatial Transcriptomics. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210513-122736659

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Abstract

The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors depends on the spatial organization of their cells. In the past decade high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that leverage spatial gene expression data to identify genes with spatial patterns and to delineate neighborhoods within tissues. To assess the ability and potential of spatial gene expression technologies to drive biological discovery, we present a curated database of literature on spatial transcriptomics dating back to 1987, along with a thorough analysis of trends in the field such as usage of experimental techniques, species, tissues studied and computational approaches used. Our analysis places current methods in historical context, and we derive insights about the field that can guide current research strategies. A companion supplement offers a more detailed look at the technologies and methods analyzed: https://pachterlab.github.io/LP_2021/.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.05.11.443152DOIDiscussion Paper
https://github.com/pachterlab/LP_2021Related ItemCode
https://doi.org/10.5281/zenodo.4795375DOICode
https://docs.google.com/spreadsheets/d/1sJDb9B7AtYmfKv4-m8XR7uc3XXw_k4kGSout8cqZ8bY/Related ItemCurated Database
ORCID:
AuthorORCID
Moses, Lambda0000-0002-7092-9427
Pachter, Lior0000-0002-9164-6231
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license. Version 1 - May 12, 2021; Version 2 - May 25, 2021. Code and data availability: All code for generating the figures is available at https://github.com/pachterlab/LP_2021, and the version as of submission is archived at https://doi.org/10.5281/zenodo.4795375. The curated database can be accessed at https://docs.google.com/spreadsheets/d/1sJDb9B7AtYmfKv4-m8XR7uc3XXw_k4kGSout8cqZ8bY/. The authors have declared no competing interest.
Record Number:CaltechAUTHORS:20210513-122736659
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210513-122736659
Official Citation:Museum of Spatial Transcriptomics. Lambda Moses, Lior Pachter. bioRxiv 2021.05.11.443152; doi: https://doi.org/10.1101/2021.05.11.443152
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109117
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:13 May 2021 19:45
Last Modified:27 May 2021 17:02

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