TY - JOUR
T1 - High-depth spatial transcriptome analysis by photo-isolation chemistry
AU - Honda, Mizuki
AU - Oki, Shinya
AU - Kimura, Ryuichi
AU - Harada, Akihito
AU - Maehara, Kazumitsu
AU - Tanaka, Kaori
AU - Meno, Chikara
AU - Ohkawa, Yasuyuki
N1 - Funding Information:
We are grateful to the staff of Ohkawa/Meno Laboratory in Kyushu University and Yumi Sugahara and Prof. Shu Narumiya in Kyoto university for technical support and discussion, and also thank the Advanced Computational Scientific Programme of the Research Institute for Information Technology, Kyushu University. We additionally thank Jeremy Allen, PhD, from Edanz (https://jp.edanz.com/ac) for editing a draft of this manuscript. This work was supported by MEXT/JSPS KAKENHI (JP19K22398 to M.H.; JP19H03424 to S.O.; JP25116010, JP17H03608, JP17K19356, JP18H04802 and JP18H05527 to Y.O.; JP16H01219, JP15K18457 and JP18K19432 to A.H.; JP16K18479, JP16H01577, JP16H01550 and JP18H04904 to K.M.), JST ACT-X (JPMJAX201D to M. H.), JST PRESTO (JPMJPR1942 to S.O.) and JST CREST (JPMJCR16G1 to Y.O.).
Publisher Copyright:
© 2021, The Author(s).
PY - 2021/12
Y1 - 2021/12
N2 - In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions.
AB - In multicellular organisms, expression profiling in spatially defined regions is crucial to elucidate cell interactions and functions. Here, we establish a transcriptome profiling method coupled with photo-isolation chemistry (PIC) that allows the determination of expression profiles specifically from photo-irradiated regions of interest. PIC uses photo-caged oligodeoxynucleotides for in situ reverse transcription. PIC transcriptome analysis detects genes specifically expressed in small distinct areas of the mouse embryo. Photo-irradiation of single cells demonstrated that approximately 8,000 genes were detected with 7 × 104 unique read counts. Furthermore, PIC transcriptome analysis is applicable to the subcellular and subnuclear microstructures (stress granules and nuclear speckles, respectively), where hundreds of genes can be detected as being specifically localised. The spatial density of the read counts is higher than 100 per square micrometre. Thus, PIC enables high-depth transcriptome profiles to be determined from limited regions up to subcellular and subnuclear resolutions.
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U2 - 10.1038/s41467-021-24691-8
DO - 10.1038/s41467-021-24691-8
M3 - Article
C2 - 34285220
AN - SCOPUS:85110947201
VL - 12
JO - Nature Communications
JF - Nature Communications
SN - 2041-1723
IS - 1
M1 - 4416
ER -