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Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

Author

Listed:
  • Susanne Nichterwitz

    (Karolinska Institutet)

  • Geng Chen

    (Department of Cell and Molecular Biology)

  • Julio Aguila Benitez

    (Karolinska Institutet)

  • Marlene Yilmaz

    (Department of Cell and Molecular Biology)

  • Helena Storvall

    (Department of Cell and Molecular Biology
    Ludwig Institute for Cancer Research)

  • Ming Cao

    (Karolinska Institutet)

  • Rickard Sandberg

    (Department of Cell and Molecular Biology
    Ludwig Institute for Cancer Research)

  • Qiaolin Deng

    (Department of Cell and Molecular Biology)

  • Eva Hedlund

    (Karolinska Institutet)

Abstract

Laser capture microscopy (LCM) coupled with global transcriptome profiling could enable precise analyses of cell populations without the need for tissue dissociation, but has so far required relatively large numbers of cells. Here we report a robust and highly efficient strategy for LCM coupled with full-length mRNA-sequencing (LCM-seq) developed for single-cell transcriptomics. Fixed cells are subjected to direct lysis without RNA extraction, which both simplifies the experimental procedures as well as lowers technical noise. We apply LCM-seq on neurons isolated from mouse tissues, human post-mortem tissues, and illustrate its utility down to single captured cells. Importantly, we demonstrate that LCM-seq can provide biological insight on highly similar neuronal populations, including motor neurons isolated from different levels of the mouse spinal cord, as well as human midbrain dopamine neurons of the substantia nigra compacta and the ventral tegmental area.

Suggested Citation

  • Susanne Nichterwitz & Geng Chen & Julio Aguila Benitez & Marlene Yilmaz & Helena Storvall & Ming Cao & Rickard Sandberg & Qiaolin Deng & Eva Hedlund, 2016. "Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    • Handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12139
    DOI: 10.1038/ncomms12139
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    Cited by:

    1. Jingyang Qian & Hudong Bao & Xin Shao & Yin Fang & Jie Liao & Zhuo Chen & Chengyu Li & Wenbo Guo & Yining Hu & Anyao Li & Yue Yao & Xiaohui Fan & Yiyu Cheng, 2024. "Simulating multiple variability in spatially resolved transcriptomics with scCube," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    2. Zhenhua Liu & Nannan Yang & Jie Dong & Wotu Tian & Lisa Chang & Jinghong Ma & Jifeng Guo & Jieqiong Tan & Ao Dong & Kaikai He & Jingheng Zhou & Resat Cinar & Junbing Wu & Armando G. Salinas & Lixin Su, 2022. "Deficiency in endocannabinoid synthase DAGLB contributes to early onset Parkinsonism and murine nigral dopaminergic neuron dysfunction," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    3. Jie Liao & Jingyang Qian & Yin Fang & Zhuo Chen & Xiang Zhuang & Ningyu Zhang & Xin Shao & Yining Hu & Penghui Yang & Junyun Cheng & Yang Hu & Lingqi Yu & Haihong Yang & Jinlu Zhang & Xiaoyan Lu & Li , 2022. "De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    4. Ke Zhang & Wanwan Feng & Peng Wang, 2022. "Identification of spatially variable genes with graph cuts," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    5. Amos C. Lee & Yongju Lee & Ahyoun Choi & Han-Byoel Lee & Kyoungseob Shin & Hyunho Lee & Ji Young Kim & Han Suk Ryu & Hoe Suk Kim & Seung Yeon Ryu & Sangeun Lee & Jong-Ho Cheun & Duck Kyun Yoo & Sumin , 2022. "Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches," Nature Communications, Nature, vol. 13(1), pages 1-12, December.

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