Smart-3SEQ

Smart-3SEQ is an RNA sequencing method that enables accurate quantification of gene expression from small and degraded RNA samples, such as those obtained from formalin-fixed paraffin-embedded (FFPE) tissue. The key features and applications of Smart-3SEQ are:

1. It can effectively characterize small samples extracted by laser-capture microdissection (LCM) from FFPE tissue.

2. Smart-3SEQ can obtain distinct biological profiles from FFPE single cells, previously impossible with other RNA-seq protocols.

3. The method has been used to identify potential new macrophage phenotypes associated with the tumor microenvironment.

4. Smart-3SEQ is highly cost-effective, enabling large gene expression profiling experiments that are not limited by sample size or tissue availability.

5. The compatibility of Smart-3SEQ with FFPE tissue allows researchers to access a vast number of archived clinical samples for study.

6. When combined with LCM, Smart-3SEQ enables unprecedented studies of small cell populations and single cells isolated by their in situ context.

Topic

RNA-Seq;Gene expression;Gene transcripts

Detail

  • Operation: Copy number estimation;Expression analysis;PCR primer design

  • Software interface: Command-line user interface

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The National Cancer Institute of the National Institutes of Health, the Ludmer Centre for Neuroinformatics and Mental Health, Foundation Multi-Investigator Research Initiative (MIRI) grant from Brain Canada.

  • Input: -

  • Output: -

  • Contact: Joseph W. Foley jwfoley@stanford.edu

  • Collection: -

  • Maturity: -

Publications

  • Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ.
  • Foley JW, et al. Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ. 2019; 29:1816-1825. doi: 10.1101/gr.234807.118
  • https://doi.org/10.1101/GR.234807.118
  • PMID: 31519740
  • PMC: PMC6836736

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