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Autonomous combinatorial color barcoding for multiplexing single molecule RNA visualization

View ORCID ProfileYong-Sheng Cheng, Yue Zhuo, Katharina Hartmann, Peng Zou, Gözde Bekki, Heike Alter, Hai-Kun Liu
doi: https://doi.org/10.1101/127373
Yong-Sheng Cheng
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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  • ORCID record for Yong-Sheng Cheng
  • For correspondence: yongsheng.cheng@dkfz.de l.haikun@dkfz.de
Yue Zhuo
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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Katharina Hartmann
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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Peng Zou
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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Gözde Bekki
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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Heike Alter
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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Hai-Kun Liu
1Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany.
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  • For correspondence: yongsheng.cheng@dkfz.de l.haikun@dkfz.de
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Abstract

Single molecular fluorescence in situ hybridization (smFISH) detects RNA transcripts with spatial information and digital molecular counting. However, the broad usage of smFISH is still hindered by the complex chemical probe conjugation or microscopy set-up, especially for investigating multiple gene expression. Here we present a multiple fluorophore enzymatic labeling method (termed HuluFISH) for smFISH probes to achieve flexible combinatorial color barcoding in single hybridization step. The multiplex capacity of HuluFISH follows an exponential growth with the increase of the number of fluorophore types. We demonstrate that this method can be used to detect cellular heterogeneity in embryonic mouse brain on single cell level.

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Posted April 18, 2017.
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Autonomous combinatorial color barcoding for multiplexing single molecule RNA visualization
Yong-Sheng Cheng, Yue Zhuo, Katharina Hartmann, Peng Zou, Gözde Bekki, Heike Alter, Hai-Kun Liu
bioRxiv 127373; doi: https://doi.org/10.1101/127373
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Autonomous combinatorial color barcoding for multiplexing single molecule RNA visualization
Yong-Sheng Cheng, Yue Zhuo, Katharina Hartmann, Peng Zou, Gözde Bekki, Heike Alter, Hai-Kun Liu
bioRxiv 127373; doi: https://doi.org/10.1101/127373

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