ArticleGenome biology2018
Holo-Seq: single-cell sequencing of holo-transcriptome.
Article in Genome biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
28 citing papers in PubMed.
- MicroRNAs in oncology: a translational perspective in the era of AI.Nature reviews. Clinical oncology · 2026Review
- bayesReact: expression-coupled regulatory motif analysis detects microRNA activity across cancers, tissues, and at the single-cell level.Nucleic acids research · 2026Article
- MicroRNAs and Their Profiling via Single-Cell Sequencing Technologies.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Single-cell microRNA-mRNA co-sequencing techniques convey large potential for understanding microRNA regulations but require careful and systemic approaches.Nature communications · 2025Article
- Mild and ultrafast GLORI enables absolute quantification of mNature methods · 2025Article
- The human genome encodes a multitude of novel miRNAs.Nucleic acids research · 2025Article
- Inferring single-cell and spatial microRNA activity from transcriptomics data.Communications biology · 2025Article
- Integrated analysis of miRNAs and mRNAs in thousands of single cells.Scientific reports · 2025Article
- RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.Genomics, proteomics & bioinformatics · 2024Article
- Transcriptome and Temporal Transcriptome Analyses in Single Cells.International journal of molecular sciences · 2024Review
- MiRNAs from the Dlk1-Dio3 locus and miR-224/452 cluster contribute to glioblastoma tumor heterogeneity.Scientific reports · 2024Article
- The Emerging Role of Super-enhancers as Therapeutic Targets in The Digestive System Tumors.International journal of biological sciences · 2023Review
- Beyond the Code: Noncoding RNAs in Skin Wound Healing.Cold Spring Harbor perspectives in biology · 2022Article
- A comparative analysis of single cell small RNA sequencing data reveals heterogeneous isomiR expression and regulation.Scientific reports · 2022Article
- Single-Cell Sequencing Identifies the Heterogeneity of CD8+ T Cells and Novel Biomarker Genes in Hepatocellular Carcinoma.Journal of healthcare engineering · 2022Article
- Single-Cell Sequencing and Its Applications in Liver Cancer.Frontiers in oncology · 2022Review
- Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects.Briefings in bioinformatics · 2021Article
- Cross-species RNA-seq for deciphering host-microbe interactions.Nature reviews. Genetics · 2021Review
- miRNA activity inferred from single cell mRNA expression.Scientific reports · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Current single-cell RNA-seq approaches are hindered by preamplification bias, loss of strand of origin information, and the inability to observe small-RNA and mRNA dual transcriptomes. Here, we introduce a single-cell holo-transcriptome sequencing (Holo-Seq) that overcomes all three hurdles. Holo-Seq has the same quantitative accuracy and uniform coverage with a complete strand of origin information as bulk RNA-seq. Most importantly, Holo-Seq can simultaneously observe small RNAs and mRNAs in a single cell. Furthermore, we acquire small RNA and mRNA dual transcriptomes of 32 human hepatocellular carcinoma single cells, which display the genome-wide super-enhancer activity and hepatic neoplasm kinetics of these cells.
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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.