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

Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection

Xiaodan Zhang, Chuansheng Hu, Chen Huang, Ying Wei, Xiaowei Li, Miaomiao Hu, Hua Li, Ji Wu, Daniel M. Czajkowsky, Yan Guo, Zhifeng Shao
doi: https://doi.org/10.1101/2021.07.13.452123
Xiaodan Zhang
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chuansheng Hu
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chen Huang
2Department of Gastrointestinal Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ying Wei
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiaowei Li
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Miaomiao Hu
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hua Li
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Ji Wu
3Bio-X Institute, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Daniel M. Czajkowsky
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: dczaj@sjtu.edu.cn yanguo@sjtu.edu.cn zfshao@sjtu.edu.cn
Yan Guo
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: dczaj@sjtu.edu.cn yanguo@sjtu.edu.cn zfshao@sjtu.edu.cn
Zhifeng Shao
1State Key Laboratory of Oncogenes and Related Genes, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: dczaj@sjtu.edu.cn yanguo@sjtu.edu.cn zfshao@sjtu.edu.cn
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

The functioning of tissues is fundamentally dependent upon not only the phenotypes of the constituent cells but also their spatial organization in the tissue. However, obtaining comprehensive transcriptomic data based on established phenotypes while retaining this spatial information has been challenging. Here we present a general and robust method based on immunofluorescence-guided laser capture microdissection (immuno-LCM-RNAseq) to enable acquisition of finely resolved spatial transcriptomes with as few as tens of cells from snap-frozen or RNAlater-treated tissues, overcoming the long-standing problem of significant RNA degradation during this lengthy process. The efficacy of this approach is exemplified by the characterization of differences at the transcript isoform level between cells at the tip versus the main capillary body of the mouse small intestine lacteal. With the extensive repertoire of phenotype-specific antibodies that are presently available, our method provides a powerful means by which spatially resolved cellular states can be delineated in situ with preserved tissues. Moreover, such high quality spatial transcriptomes defined by immuno-markers can be used to compare with clusters obtained from single-cell RNAseq studies of dissociated cells as well as applied to bead-based spatial transcriptomics approaches that require such information a priori for cell identification.

Competing Interest Statement

The authors have declared no competing interest.

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-ND 4.0 International license.
Back to top
PreviousNext
Posted July 14, 2021.
Download PDF

Supplementary Material

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.
Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection
(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
Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection
Xiaodan Zhang, Chuansheng Hu, Chen Huang, Ying Wei, Xiaowei Li, Miaomiao Hu, Hua Li, Ji Wu, Daniel M. Czajkowsky, Yan Guo, Zhifeng Shao
bioRxiv 2021.07.13.452123; doi: https://doi.org/10.1101/2021.07.13.452123
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Robust Acquisition of High Resolution Spatial Transcriptomes from Preserved Tissues with Immunofluorescence Based Laser Capture Microdissection
Xiaodan Zhang, Chuansheng Hu, Chen Huang, Ying Wei, Xiaowei Li, Miaomiao Hu, Hua Li, Ji Wu, Daniel M. Czajkowsky, Yan Guo, Zhifeng Shao
bioRxiv 2021.07.13.452123; doi: https://doi.org/10.1101/2021.07.13.452123

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

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3698)
  • Biochemistry (7809)
  • Bioengineering (5689)
  • Bioinformatics (21330)
  • Biophysics (10595)
  • Cancer Biology (8199)
  • Cell Biology (11961)
  • Clinical Trials (138)
  • Developmental Biology (6777)
  • Ecology (10419)
  • Epidemiology (2065)
  • Evolutionary Biology (13900)
  • Genetics (9726)
  • Genomics (13094)
  • Immunology (8164)
  • Microbiology (20058)
  • Molecular Biology (7871)
  • Neuroscience (43147)
  • Paleontology (321)
  • Pathology (1280)
  • Pharmacology and Toxicology (2264)
  • Physiology (3362)
  • Plant Biology (7246)
  • Scientific Communication and Education (1315)
  • Synthetic Biology (2010)
  • Systems Biology (5547)
  • Zoology (1132)