Publications with SCRINSHOT

Postnatal FGF-signalling establishes gradients of cell-identities along the proximal-distal axis of the lung airways
Alexandros Sountoulidis, Alexandra Firsova, Andreas Liontos, Jonas Theelke, Janine Koepke, Pamela Millar-Büchner, Louise Mannerås-Holm, Åsa Björklund, Athanasios Fysikopoulos, Konstantin Gaengel, Fredrik Bäckhed, Christer Betsholtz, Werner Seeger, Saverio Bellusci, Christos Samakovlis
2023, bioRxiv – Preprint https://doi.org/10.1101/2023.12.11.571142
Here, we used SCRINSHOT to show the activation a graded gene-expression programs along the proximal-distal axis of mouse lung epithelium.

Pooled optical screening in bacteria using chromosomally expressed barcodes
Ruben R. G. Soares, Daniela A. García-Soriano, Jimmy Larsson, David Fange, Dvir Schirman, Marco Grillo, Anna Knöppel, Beer Chakra Sen, Fabian Svahn, Spartak Zikrin, Mats Nilsson, Johan Elf
2023, bioRxiv – Preprint https://doi.org/10.1101/2023.11.17.567382
The authors used SplintR ligase, as initially introduced by SCRINSHOT, to ligate Padlock probes for in situ genotyping of libraries with genomic barcodes in Escherichia coli.

Rapid and signal crowdedness-robust in situ sequencing through hybrid block coding
Tianyi Chang, Wuji Han, Mengcheng Jiang, Jizhou Li, Zhizhao Liao, Mingchuan Tang, Jianyun Zhang, Jie Shen, Zitian Chen, Peng Fei, Xianwen Ren, Yuhong Pang, Guanbo Wang, Jianbin Wang, Yanyi Huang
2023, Proceedings of the National Academy of Sciences of the United States of America – Article https://doi.org/10.1073/pnas.2309227120
The authors used the sequencing-by-synthesis (SBS) chemistry and microfluidics to speed up the signal detection by SCRINSHOT.

Deciphering a critical role of uterine epithelial SHP2 in parturition initiation at single cell resolution
Meng Liu, Mengjun Ji, Jianghong Cheng, Yingzhe Li, Yingpu Tian, Hui Zhao, Yang Wang, Sijing Zhu, Leilei Zhang, Xinmei Xu, Gen-Sheng Feng, Xiaohuan Liang, Haili Bao, Yedong Tang, Shuangbo Kong, Jinhua Lu, Haibin Wang, Zhongxian Lu, Wenbo Deng
2023, Nature Communications – Article https://doi.org/10.1038/s41467-023-43102-8
The authors used SCRINSHOT to detect Cox1 and Akr1b3 in uterine epithelium.

A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung
Alexandros Sountoulidis, Sergio Marco Salas, Emelie Braun, Christophe Avenel, Joseph Bergenstråhle, Jonas Theelke, Marco Vicari, Paulo Czarnewski, Andreas Liontos, Xesus Abalo, Žaneta Andrusivová, Reza Mirzazadeh, Michaela Asp, Xiaofei Li, Lijuan Hu, Sanem Sariyar, Anna Martinez Casals, Burcu Ayoglu, Alexandra Firsova, Jakob Michaëlsson, Emma Lundberg, Carolina Wählby, Erik Sundström, Sten Linnarsson, Joakim Lundeberg, Mats Nilsson, Christos Samakovlis
2023, Nature Cell Biology – Article https://doi.org/10.1038/s41556-022-01064-x
Here, we used SCRINSHOT to analyze the spatial distribution of lung neuroendocrine cell states in the human fetal lung.

PRDM16 functions as a co-repressor in the BMP pathway to suppress neural stem cell proliferation
Li He, Jiayu Wen, Qi Dai
2023, bioRxiv – Preprint https://doi.org/10.1101/2023.01.13.523917

Probe set selection for targeted spatial transcriptomics
Louis B. Kuemmerle, Malte D. Luecken, Alexandra B. Firsova, Lisa Barros de Andrade e Sousa, Lena Straßer, Lukas Heumos, Ilhem Isra Mekki, Krishnaa T. Mahbubani, Alexandros Sountoulidis, Tamás Balassa, Ferenc Kovacs, Peter Horvath, Marie Piraud, Ali Ertürk, Christos Samakovlis, Fabian J. Theis
2022, bioRxiv – Preprint https://doi.org/10.1101/2022.08.16.504115
Here, we used SCRINSHOT to validate the efficiency of a new bioinformatics tool for marker selection. This allows the spatial validation of scRNA-Seq analysis results.

An essential function for autocrine Hedgehog signaling in epithelial proliferation and differentiation in the trachea
Wenguang Yin, Andreas Liontos, Janine Koepke, Maroua Ghoul, Luciana Mazzocchi, Xinyuan Liu, Chunyan Lu, Haoyu Wu, Athanasios Fysikopoulos, Alexandros Sountoulidis, Werner Seeger, Clemens Ruppert, Andreas Günther, Didier Y.R. Stainier, Christos Samakovlis
2022, Development – Article https://doi.org/10.1242/dev.199804
Here, we used SCRINSHOT to detect various HH-singaling components in the developing mouse trachea.

MEG8 regulates Tissue Factor Pathway Inhibitor 2 (TFPI2) expression in the endothelium
Veerle Kremer, Diewertje I. Bink, Laura Stanicek, Eva van Ingen, Theresa Gimbel, Sarah Hilderink, Stefan Günther, Anne Yaël Nossent, Reinier A. Boon
2022, Scientific Reports – Article https://doi.org/10.1038/s41598-022-04812-z
The authors used SCRINSHOT to detect MEG8 long non-coding RNA in in vitro culture assays.