ArticleNucleic acids research2021
Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed, 63 citations in OpenAlex.
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Spheroids and organoids to study long noncoding RNAs in cancer: how they could replace animal models.Cancer metastasis reviews · 2026Review
- InSituPREP enables 3D single-cell mapping of interaction-associated gene programs in the breast cancer tumor microenvironment.Nucleic acids research · 2026Article
- ModelistsGCN: a multimodal graph convolutional network framework for single-cell spatial transcriptomic cell typing.Briefings in bioinformatics · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- HMC3 revealed: how much do these "Microglia" really tell us?Frontiers in immunology · 2026Review
- High-plex spatial RNA imaging in one round with conventional microscopes using color-intensity barcodes.Nature biotechnology · 2025Article
- Protocol optimization improves the performance of multiplexed RNA imaging.Scientific reports · 2025Article
- Visualizing the transcription and replication of influenza A viral RNAs in cells by multiple direct RNA padlock probing and in situ sequencing (mudRapp-seq).Nucleic acids research · 2025Article
- A platform for multimodalbioRxiv : the preprint server for biology · 2025Article
- Spatial multi-omics at subcellular resolution via high-throughput in situ pairwise sequencing.Nature biomedical engineering · 2024Article
- Computational analysis of super-resolved in situ sequencing data reveals genes modified by immune-tumor contact events.RNA (New York, N.Y.) · 2024Article
- Rapid and signal crowdedness-robust in situ sequencing through hybrid block coding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Enablers and challenges of spatial omics, a melting pot of technologies.Molecular systems biology · 2023Review
- Spatial Transcriptomics: Emerging Technologies in Tissue Gene Expression Profiling.Analytical chemistry · 2023Review
- Spatial transcriptomics in development and disease.Molecular biomedicine · 2023Review
- lhCLIP reveals the in vivo RNA-RNA interactions recognized by hnRNPK.PLoS genetics · 2023Article
- Spatial transcriptomics for profiling the tropism of viral vectors in tissues.Nature biotechnology · 2023Article
- Spatial transcriptomics: recent developments and insights in respiratory research.Military Medical Research · 2023Review
- Deconvolution of spatial sequencing provides accurate characterization of hESC-derived DA transplantsMolecular therapy. Methods & clinical development · 2023Article
Corrections and comments
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Authors and funding
25 authors at 4 institutions in 2 countries.
Funding
Abstract
We present barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel insitu analyses (BOLORAMIS), a reverse transcription-free method for spatially-resolved, targeted, in situ RNA identification of single or multiple targets. BOLORAMIS was demonstrated on a range of cell types and human cerebral organoids. Singleplex experiments to detect coding and non-coding RNAs in human iPSCs showed a stem-cell signature pattern. Specificity of BOLORAMIS was found to be 92% as illustrated by a clear distinction between human and mouse housekeeping genes in a co-culture system, as well as by recapitulation of subcellular localization of lncRNA MALAT1. Sensitivity of BOLORAMIS was quantified by comparing with single molecule FISH experiments and found to be 11%, 12% and 35% for GAPDH, TFRC and POLR2A, respectively. To demonstrate BOLORAMIS for multiplexed gene analysis, we targeted 96 mRNAs within a co-culture of iNGN neurons and HMC3 human microglial cells. We used fluorescence in situ sequencing to detect error-robust 8-base barcodes associated with each of these genes. We then used this data to uncover the spatial relationship among cells and transcripts by performing single-cell clustering and gene-gene proximity analyses. We anticipate the BOLORAMIS technology for in situ RNA detection to find applications in basic and translational research.
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Registered trials
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.