ArticleNucleic acids research2018
Efficient in situ barcode sequencing using padlock probe-based BaristaSeq.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 123 papers.
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Who cites it
123 citing papers in PubMed.
- Integrative single-cell and spatial transcriptomic approaches to decipher the tumor microenvironment and therapeutic resistance in pancreatic cancer.Cancer biology & therapy · 2026Review
- 3D multi-omics tumour atlases: from technology to biology and clinical translation.Nature reviews. Cancer · 2026Review
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Deep Learning-Assisted Prioritization of Candidate Drug Targets in Tumors Using Spatial Multi-Omics.Biology · 2026Review
- Selective collateralization of transcriptomically distinct neurons organizes visual-stream output from the primary visual cortex.bioRxiv : the preprint server for biology · 2026Article
- A multiperspective evaluation framework of spatial transcriptomics clustering methods.NAR genomics and bioinformatics · 2026Article
- Spatial omics illuminates tumor heterogeneity.Cell reports methods · 2026Review
- Dissecting human organ development using spatial technologies.Developmental cell · 2026Review
- BARseq3: a modular system for integrating spatial multi-omics and cellular barcoding in single cells.bioRxiv : the preprint server for biology · 2026Article
- Spatial profiling of gene editing by in situ sequencing in mice and macaques.Nature biomedical engineering · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Scalable discovery of spatial multicellular patterns via neighborhood-to-sequence transformation.Communications biology · 2026Article
- The Evolution of Spatial Omics Technologies Introduces A Novel Avenue for Lung Cancer Research.Genomics, proteomics & bioinformatics · 2026Review
- Article
- Developing a Robust Multiround HCR-FISH Method Modified for Caenorhabditis elegans.Genes to cells : devoted to molecular & cellular mechanisms · 2026Article
- CEMUSA: a graph-based integrative metric for evaluating clusters in spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- SpaLSTF: Diffusion-based generative model with BiLSTM and XCA-Transformer for spatial transcriptomics imputation.PLoS computational biology · 2026Article
- MMSpa is a deep learning-based tool that enhances the identification of spatial domains in spatial transcriptomics studies.PLoS biology · 2026Article
- Applications and development of in situ nucleic acid visualization techniques.Frontiers in bioengineering and biotechnology · 2026Review
- Vector-guided graph learning for spatial multi-slice multi-omics alignment.Cell reports methods · 2025Article
63 more citing papers are in PubMed but not listed here.
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5 authors.
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Abstract
Cellular DNA/RNA tags (barcodes) allow for multiplexed cell lineage tracing and neuronal projection mapping with cellular resolution. Conventional approaches to reading out cellular barcodes trade off spatial resolution with throughput. Bulk sequencing achieves high throughput but sacrifices spatial resolution, whereas manual cell picking has low throughput. In situ sequencing could potentially achieve both high spatial resolution and high throughput, but current in situ sequencing techniques are inefficient at reading out cellular barcodes. Here we describe BaristaSeq, an optimization of a targeted, padlock probe-based technique for in situ barcode sequencing compatible with Illumina sequencing chemistry. BaristaSeq results in a five-fold increase in amplification efficiency, with a sequencing accuracy of at least 97%. BaristaSeq could be used for barcode-assisted lineage tracing, and to map long-range neuronal projections.
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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.