Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

Mizuki Honda; Ryuichi Kimura; Akihito Harada; Kazumitsu Maehara; Kaori Tanaka; Yasuyuki Ohkawa; Shinya Oki

doi:10.1016/j.xpro.2022.101346

Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

Mizuki Honda, Ryuichi Kimura, Akihito Harada, Kazumitsu Maehara, Kaori Tanaka, Yasuyuki Ohkawa, Shinya Oki

Research output: Contribution to journal › Article › peer-review

Abstract

Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types. For complete details on the use and execution of this protocol, please refer to Honda et al. (2021).

Original language	English
Article number	101346
Journal	STAR Protocols
Volume	3
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2022.101346
Publication status	Published - Jun 17 2022

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)
Neuroscience(all)
Immunology and Microbiology(all)
Medicine(all)

Access to Document

10.1016/j.xpro.2022.101346

Cite this

@article{e733ba3e3cd0422c8ad7a3701ccefae8,

title = "Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections",

abstract = "Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types. For complete details on the use and execution of this protocol, please refer to Honda et al. (2021).",

author = "Mizuki Honda and Ryuichi Kimura and Akihito Harada and Kazumitsu Maehara and Kaori Tanaka and Yasuyuki Ohkawa and Shinya Oki",

note = "Funding Information: We are grateful to the staff of Ohkawa and Oki Laboratories, especially to Yumi Sugahara for technical support and Prof. Shu Narumiya at Kyoto University for discussion, as well as Intensively Promoted Projects by the Research Institute for Information Technology, Kyushu University. This work was supported by MEXT / JSPS KAKENHI ( JP19K22398 to M.H.; JP19H03424 to S.O.; JP18H04802 , JP18H05527 , JP19H05244 , JP20K21398 , JP20H00456 , and JP20H04846 to Y.O.; JP18K19432 , JP19H03211 , JP19H05425 , JP20H05368 , JP21H00430 , and JP21H05292 to A.H.; JP19H04970 , JP19H03158 , JP20H05393 , and JP21H05755 to K.M.), JST ACT-X ( JPMJAX201D to M.H.), JST PRESTO ( JPMJPR1942 to S.O., JPMJPR19K7 to A.H., JPMJPR2026 to K.M.), JST ERATO ( JPMJER2101 to S.O.), JST CREST ( JPMJCR16G1 to Y.O.), and AMED JP20ek0109489h0001 to Y.O. Funding Information: We are grateful to the staff of Ohkawa and Oki Laboratories, especially to Yumi Sugahara for technical support and Prof. Shu Narumiya at Kyoto University for discussion, as well as Intensively Promoted Projects by the Research Institute for Information Technology, Kyushu University. This work was supported by MEXT/JSPS KAKENHI (JP19K22398 to M.H.; JP19H03424 to S.O.; JP18H04802, JP18H05527, JP19H05244, JP20K21398, JP20H00456, and JP20H04846 to Y.O.; JP18K19432, JP19H03211, JP19H05425, JP20H05368, JP21H00430, and JP21H05292 to A.H.; JP19H04970, JP19H03158, JP20H05393, and JP21H05755 to K.M.), JST ACT-X (JPMJAX201D to M.H.), JST PRESTO (JPMJPR1942 to S.O. JPMJPR19K7 to A.H. JPMJPR2026 to K.M.), JST ERATO (JPMJER2101 to S.O.), JST CREST (JPMJCR16G1 to Y.O.), and AMED JP20ek0109489h0001 to Y.O. Y.O. and S.O. conceived the PIC and supervised all aspects of the work. M.H. R.K. and A.H. performed the experiments. M.H. K.M. K.T. Y.O. and S.O. analyzed the sequencing data. M.H. Y.O. and S.O. wrote the manuscript. All authors read and approved the final manuscript. S.O. and Y.O. are involved in a pending patent related to PIC technology (application number, 2019-094216; patent office, Japan Patent Office; current status, patent pending). All the other authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022 The Author(s)",

year = "2022",

month = jun,

day = "17",

doi = "10.1016/j.xpro.2022.101346",

language = "English",

volume = "3",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "2",

}

TY - JOUR

T1 - Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

AU - Honda, Mizuki

AU - Kimura, Ryuichi

AU - Harada, Akihito

AU - Maehara, Kazumitsu

AU - Tanaka, Kaori

AU - Ohkawa, Yasuyuki

AU - Oki, Shinya

N1 - Funding Information: We are grateful to the staff of Ohkawa and Oki Laboratories, especially to Yumi Sugahara for technical support and Prof. Shu Narumiya at Kyoto University for discussion, as well as Intensively Promoted Projects by the Research Institute for Information Technology, Kyushu University. This work was supported by MEXT / JSPS KAKENHI ( JP19K22398 to M.H.; JP19H03424 to S.O.; JP18H04802 , JP18H05527 , JP19H05244 , JP20K21398 , JP20H00456 , and JP20H04846 to Y.O.; JP18K19432 , JP19H03211 , JP19H05425 , JP20H05368 , JP21H00430 , and JP21H05292 to A.H.; JP19H04970 , JP19H03158 , JP20H05393 , and JP21H05755 to K.M.), JST ACT-X ( JPMJAX201D to M.H.), JST PRESTO ( JPMJPR1942 to S.O., JPMJPR19K7 to A.H., JPMJPR2026 to K.M.), JST ERATO ( JPMJER2101 to S.O.), JST CREST ( JPMJCR16G1 to Y.O.), and AMED JP20ek0109489h0001 to Y.O. Funding Information: We are grateful to the staff of Ohkawa and Oki Laboratories, especially to Yumi Sugahara for technical support and Prof. Shu Narumiya at Kyoto University for discussion, as well as Intensively Promoted Projects by the Research Institute for Information Technology, Kyushu University. This work was supported by MEXT/JSPS KAKENHI (JP19K22398 to M.H.; JP19H03424 to S.O.; JP18H04802, JP18H05527, JP19H05244, JP20K21398, JP20H00456, and JP20H04846 to Y.O.; JP18K19432, JP19H03211, JP19H05425, JP20H05368, JP21H00430, and JP21H05292 to A.H.; JP19H04970, JP19H03158, JP20H05393, and JP21H05755 to K.M.), JST ACT-X (JPMJAX201D to M.H.), JST PRESTO (JPMJPR1942 to S.O. JPMJPR19K7 to A.H. JPMJPR2026 to K.M.), JST ERATO (JPMJER2101 to S.O.), JST CREST (JPMJCR16G1 to Y.O.), and AMED JP20ek0109489h0001 to Y.O. Y.O. and S.O. conceived the PIC and supervised all aspects of the work. M.H. R.K. and A.H. performed the experiments. M.H. K.M. K.T. Y.O. and S.O. analyzed the sequencing data. M.H. Y.O. and S.O. wrote the manuscript. All authors read and approved the final manuscript. S.O. and Y.O. are involved in a pending patent related to PIC technology (application number, 2019-094216; patent office, Japan Patent Office; current status, patent pending). All the other authors declare no competing interests. Publisher Copyright: © 2022 The Author(s)

PY - 2022/6/17

Y1 - 2022/6/17

N2 - Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types. For complete details on the use and execution of this protocol, please refer to Honda et al. (2021).

AB - Photo-isolation chemistry (PIC) enables isolation of transcriptome information from locally defined areas by photo-irradiation. Here, we present an optimized PIC protocol for formalin-fixed frozen and paraffin mouse sections and fresh-frozen mouse sections. We describe tissue section preparation and permeabilization, followed by in situ reverse transcription using photo-caged primers. We then detail immunostaining and UV-mediated uncaging to the target areas, followed by linear amplification of uncaged cDNAs, library preparation, and quantification. This protocol can be applied to various animal tissue types. For complete details on the use and execution of this protocol, please refer to Honda et al. (2021).

UR - http://www.scopus.com/inward/record.url?scp=85129412627&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85129412627&partnerID=8YFLogxK

U2 - 10.1016/j.xpro.2022.101346

DO - 10.1016/j.xpro.2022.101346

M3 - Article

C2 - 35496796

AN - SCOPUS:85129412627

SN - 2666-1667

VL - 3

JO - STAR Protocols

JF - STAR Protocols

IS - 2

M1 - 101346

ER -

Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections

Abstract

All Science Journal Classification (ASJC) codes

Access to Document

Other files and links

Fingerprint

Cite this