TY - JOUR
T1 - Whole-brain spatial transcriptional analysis at cellular resolution
AU - Kanatani, Shigeaki
AU - Kreutzmann, Judith C.
AU - Li, Yue
AU - West, Zoe
AU - Larsen, Lea Lydolph
AU - Nikou, Danai Vougesi
AU - Eidhof, Ilse
AU - Walton, Abigail
AU - Zhang, Songbai
AU - Rodríguez-Kirby, Leslie Rubio
AU - Skytte, Jacob Lercke
AU - Salinas, Casper Gravesen
AU - Takamatsu, Kimiharu
AU - Li, Xiaofei
AU - Tanaka, Daisuke H.
AU - Kaczynska, Dagmara
AU - Fukumoto, Keishiro
AU - Karamzadeh, Razieh
AU - Xiang, Yujiao
AU - Uesaka, Naofumi
AU - Tanabe, Tsutomu
AU - Adner, Mikael
AU - Hartman, Johan
AU - Miyakawa, Ayako
AU - Sundström, Erik
AU - Castelo-Branco, Gonçalo
AU - Roostalu, Urmas
AU - Hecksher-Sørensen, Jacob
AU - Uhlén, Per
N1 - Publisher Copyright:
© 2024 the authors, some rights reserved;
PY - 2024/11
Y1 - 2024/11
N2 - Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer–mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.
AB - Recent advances in RNA analysis have deepened our understanding of cellular states in biological tissues. However, a substantial gap remains in integrating RNA expression data with spatial context across organs, primarily owing to the challenges associated with RNA detection within intact tissue volumes. Here, we developed Tris buffer–mediated retention of in situ hybridization chain reaction signal in cleared organs (TRISCO), an effective tissue-clearing method designed for whole-brain spatial three-dimensional (3D) RNA imaging. TRISCO resolved several crucial issues, including the preservation of RNA integrity, achieving uniform RNA labeling, and enhancing tissue transparency. We tested TRISCO using a broad range of cell-identity markers, noncoding and activity-dependent RNAs, within diverse organs of varying sizes and species. TRISCO thus emerges as a powerful tool for single-cell, whole-brain, 3D imaging that enables comprehensive transcriptional spatial analysis across the entire brain.
UR - https://www.scopus.com/pages/publications/85210458728
UR - https://www.scopus.com/pages/publications/85210458728#tab=citedBy
U2 - 10.1126/science.adn9947
DO - 10.1126/science.adn9947
M3 - Article
C2 - 39571016
AN - SCOPUS:85210458728
SN - 0036-8075
VL - 386
SP - 907
EP - 915
JO - Science
JF - Science
IS - 6724
ER -