Single-Cell Capture, RNA-seq, and Transcriptome Analysis from the Neural Retina

  • Rachayata Dharmat
  • Sangbae Kim
  • Yumei Li
  • Rui ChenEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 2092)


Single-cell RNA sequencing (scRNA-seq) is an emerging technology that can address the challenge of cellular heterogeneity. In the last decade, the cost per cell has been dramatically reduced, and the throughput has been increased by 104-fold. Like many other tissues, the retina is highly heterogeneous with an estimated of over 100 subtypes of neuronal cells. Here, we describe the current techniques to perform scRNA-seq on the adult retinal tissue including retinal dissection, retinal dissociation, assessment of cell population, cDNA synthesis, library construction, and next-generation sequencing. In addition, we introduce a workflow of scRNA-seq data analysis using open-source tools.

Key words

Retinal dissection and dissociation Single-cell RNA-seq (scRNA-seq) Single-nuclei RNA-seq (snRNA-seq) ICELL8 10× Chromium Poly-(A)+ transcriptome amplification ScRNA-seq analysis 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Rachayata Dharmat
    • 1
    • 2
  • Sangbae Kim
    • 1
  • Yumei Li
    • 1
  • Rui Chen
    • 1
    • 2
    Email author
  1. 1.Human genome sequencing centerBaylor College of MedicineHoustonUSA
  2. 2.Department of molecular and Human GeneticsBaylor College of MedicineHoustonUSA

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