IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v7y2016i1d10.1038_ncomms12139.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms12139
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms12139?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. 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.
    2. 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.
    3. 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.
    4. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:7:y:2016:i:1:d:10.1038_ncomms12139. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.