Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Museum of Spatial Transcriptomics

View ORCID ProfileLambda Moses, View ORCID ProfileLior Pachter
doi: https://doi.org/10.1101/2021.05.11.443152
Lambda Moses
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lambda Moses
Lior Pachter
1Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
2Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lior Pachter
  • For correspondence: lpachter@caltech.edu
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

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/.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Figure 1 revised to include ligation mediated SNV detection and single cell cDNA amplification; Figure 3 revised to reduce confusion and correct misunderstandings per Long Cai's request; corresponding parts of the Supplement were updated reflecting the paper in a more detailed manner.

  • https://pachterlab.github.io/LP_2021

Copyright 
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.
Back to top
PreviousNext
Posted May 25, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Museum of Spatial Transcriptomics
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Museum of Spatial Transcriptomics
Lambda Moses, Lior Pachter
bioRxiv 2021.05.11.443152; doi: https://doi.org/10.1101/2021.05.11.443152
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Museum of Spatial Transcriptomics
Lambda Moses, Lior Pachter
bioRxiv 2021.05.11.443152; doi: https://doi.org/10.1101/2021.05.11.443152

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3505)
  • Biochemistry (7348)
  • Bioengineering (5324)
  • Bioinformatics (20266)
  • Biophysics (10019)
  • Cancer Biology (7744)
  • Cell Biology (11305)
  • Clinical Trials (138)
  • Developmental Biology (6437)
  • Ecology (9953)
  • Epidemiology (2065)
  • Evolutionary Biology (13325)
  • Genetics (9361)
  • Genomics (12586)
  • Immunology (7702)
  • Microbiology (19024)
  • Molecular Biology (7443)
  • Neuroscience (41041)
  • Paleontology (300)
  • Pathology (1229)
  • Pharmacology and Toxicology (2138)
  • Physiology (3161)
  • Plant Biology (6861)
  • Scientific Communication and Education (1273)
  • Synthetic Biology (1896)
  • Systems Biology (5313)
  • Zoology (1089)