ArticleScientific reports2022
Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 58 citations in OpenAlex.
- Immunophenotyping by Spatial Biology.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Spatial transcriptomics differences of histopathological growth patterns in colorectal cancer liver metastases.British journal of cancer · 2026Article
- Unveiling the role of spatial transcriptomics in the analysis of the tumor immune microenvironment (Review).International journal of molecular medicine · 2026Review
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Multimodal spatial omics: From data acquisition to computational integration.Patterns (New York, N.Y.) · 2026Review
- Imaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications.Biology · 2026Review
- Spatially resolved T cell receptor diversity mapping uncovers variability of the cancer immune microenvironment.EBioMedicine · 2026Article
- Improving Spatial Transcriptomics with Dual-Color Coding and Cell Painting.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integration of spatial and single-nucleus transcriptomics to map gene expression in the developing mouse kidney.Development (Cambridge, England) · 2025Article
- Microglia networks within the tapestry of alzheimer's disease through spatial transcriptomics.Molecular neurodegeneration · 2025Review
- Protocol optimization improves the performance of multiplexed RNA imaging.Scientific reports · 2025Article
- Spatial TCR clonality and clonal expansion in the in situ microenvironment of non-small cell lung cancer.Journal for immunotherapy of cancer · 2025Article
- Next generation lineage tracing and its applications to unravel development.NPJ systems biology and applications · 2025Review
- Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.Nature methods · 2025Article
- Spatial-Omics Methods and Applications.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Article
- Spatial-transcriptomic profiling: a new lens for understanding myelofibrosis pathophysiology.Cell communication and signaling : CCS · 2024Review
- Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
- Open-source, high-throughput targeted in situ transcriptomics for developmental and tissue biology.Development (Cambridge, England) · 2024Article
- Spatial multimodal analysis of transcriptomes and metabolomes in tissues.Nature biotechnology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Highly multiplexed spatial mapping of transcripts within tissues allows for investigation of the transcriptomic and cellular diversity of mammalian organs previously unseen. Here we explore a direct RNA (dRNA) detection approach incorporating the use of padlock probes and rolling circle amplification in combination with hybridization-based in situ sequencing chemistry. We benchmark a High Sensitivity Library Preparation Kit from CARTANA that circumvents the reverse transcription needed for cDNA-based in situ sequencing (ISS) via direct RNA detection. We found a fivefold increase in transcript detection efficiency when compared to cDNA-based ISS and also validated its multiplexing capability by targeting a curated panel of 50 genes from previous publications on mouse brain sections, leading to additional data interpretation such as de novo cell clustering. With this increased efficiency, we also found to maintain specificity, multiplexing capabilities and ease of implementation. Overall, the dRNA chemistry shows significant improvements in target detection efficiency, closing the gap to other fluorescent in situ hybridization-based technologies and opens up possibilities to explore new biological questions previously not possible with cDNA-based ISS.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.