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Zebrafish pp 93-106 | Cite as

Fluorescence-Activated Cell Sorting and Gene Expression Profiling of GFP-Positive Cells from Transgenic Zebrafish Lines

  • Hideyuki Tanabe
  • Masahide Seki
  • Mari Itoh
  • Ailani Deepak
  • Pradeep Lal
  • Terumi Horiuchi
  • Yutaka Suzuki
  • Koichi Kawakami
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1451)

Abstract

Gene expression profiling is a useful approach for deeper understanding of the specificity of cells, tissues, and organs in the transcriptional level. Recent development of high-throughput next-generation sequence (NGS) allows the RNA-seq method for this profiling. This method provides precise information of transcripts about the quantitation and the structure such as the splicing variants. In this chapter, we describe a method for gene expression profiling of GFP-positive cells from transgenic zebrafish by RNA-seq. We labeled specific cells in the brain with GFP by crossing a Gal4 driver line with the UAS:GFP line, isolated those cells by fluorescence-activated cell sorting (FACS), and analyzed by RNA-seq.

Key words

Tol2 transgenesis Gene trap Enhancer trap Gal4-UAS system GFP FACS RNA extract RNA-seq Next-generation sequence Gene expression analysis 

Notes

Acknowledgments

We thank Naoyuki Inagaki for the helpful advice about cell dissociation methods. This work was partly supported by the National BioResource Project (to KK), Grant-in-Aids for Scientific Research on Innovative Areas “Genome Science” (221S0002 to YS), and Grant-in-Aids for Scientific Research (A) (23241063 and 15H02370 to KK) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Hideyuki Tanabe
    • 1
  • Masahide Seki
    • 2
  • Mari Itoh
    • 1
  • Ailani Deepak
    • 1
    • 3
  • Pradeep Lal
    • 1
  • Terumi Horiuchi
    • 2
  • Yutaka Suzuki
    • 2
  • Koichi Kawakami
    • 1
    • 3
  1. 1.Division of Molecular and Developmental BiologyNational Institute of GeneticsMishimaJapan
  2. 2.Department of Medical Genome SciencesGraduate School of Frontier Sciences, The University of TokyoChibaJapan
  3. 3.Department of GeneticsGraduate University for Advanced Studies (SOKENDAI)MishimaJapan

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