In situ sequencing for RNA analysis in preserved tissue and cells

By Rongqin Ke, Marco Mignardi, A. Pacureanu, J. Svedlund, J. Botling, Carolina Wählby, M. Nilsson. Nature Methods, 2013

869 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/918d51d768dd78ebb8e3c6f1612f79ba1be4bfd0

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Citations in the corpus

An introduction to spatial transcriptomics for biomedical research (2022, methodology): “The first example of this for spatial transcriptomics was released in 2013, before being commercialized as Cartana [49], later purchased by 10X Genomics.”
Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies (2019, methodology): “Some of these techniques, such as targeted in situ sequencing (ISS) 8 and FISSEQ 9 , are based on in situ RNA sequencing.”
Cell segmentation in imaging-based spatial transcriptomics (2021, neutral): “These techniques are being gradually augmented by spatially resolved transcriptomics measurements based on in situ sequencing 5,6 , multiplexed single-molecule fluorescent in situ hybridization (smFISH) 7–9 or spatially barcoded hybridization 10,11 .”
Single-cell transcriptome sequencing: recent advances and remaining challenges (2016, background): “Alternatively, emerging in situ sequencing strategies are able to capture and amplify RNA within the original tissue context, although current methods can measure up to only a few dozen genes per cell 43–45 .”
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma (2017, positive): “We verified the upregulation of both NFIB and SOX9 using multiplexed in situ RNA staining, with padlock probes and rolling circle amplification (Ke et al., 2013), on sections of tumor core as well as peripheral tissue (Fig.”
Museum of spatial transcriptomics (2020, methodology): “The 2013 ISS [50], later commercialized by Cartana, uses one query base per probe as in cPAL [87] to sequence gene barcodes (Figure 2E).”
Best practices for single-cell analysis across modalities (2023, background): “Tangram 224 , GridNet 230 and eggplant 231 generate common coordinate frameworks across samples to mitigate this issue 232 .”
Genome-wide RNA Tomography in the zebrafish embryo. (2014, background): “In situ sequencing of RNA in intact tissues has the potential to provide direct information about the spatial organization of the transcriptome (Ke et al., 2013; Lee et al., 2014).”
The Human Cell Atlas (2017, neutral): “Finally, more recent studies have performed RNA-seq in situ in cells and in preserved tissue sections (Ke et al., 2013; Lee et al., 2014).”
Mapping the Mouse Cell Atlas by Microwell-Seq. (2018, neutral): “…2015; Lorthongpanich et al., 2013; Mooijman et al., 2016; Nagano et al., 2013; Smallwood et al., 2014), and in situ analysis (Chen et al., 2015; Ke et al., 2013; Lee et al., Cell 172, 1091–1107, February 22, 2018 ª 2018 Elsevier Inc. 1091 2014), may provide further information regarding…”