ArticleNature biotechnology2009
Quantification of the yeast transcriptome by single-molecule sequencing.
Article in Nature biotechnology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 107 papers, 1 of them a synthesis that pooled it.
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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
107 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of dispensable essential genes and their interactions with bypass suppressors.Life science alliance · 2024Pooled it
- Polarized anionic phospholipids and exocytosis are implicated in the polarized recruitment of budding yeast AP180, an endocytic initiator.Molecular biology of the cell · 2026Article
- A practical guide to targeted single-cell RNA sequencing technologies.Communications biology · 2026Review
- Qarles: a web server for the quick characterization of large sets of genes.NAR genomics and bioinformatics · 2025Article
- A proteome-wide yeast degron collection for the dynamic study of protein function.The Journal of cell biology · 2025Article
- YeastFab Cloning of Toxic Genes and Protein Expression Optimization in Yeast.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Exploiting phenotypic heterogeneity to improve production of glutathione by yeast.Microbial cell factories · 2024Article
- Article
- Spontaneous deamination of cytosine to uracil is biased to the non-transcribed DNA strand in yeast.DNA repair · 2023Article
- Fungal biotechnology: From yesterday to tomorrow.Frontiers in fungal biology · 2023Review
- RNAseq analysis of treatment-dependent signaling changes during inflammation in a mouse cutaneous wound healing model.BMC genomics · 2021Article
- Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast.Nucleic acids research · 2021Article
- A genome-scale yeast library with inducible expression of individual genes.Molecular systems biology · 2021Article
- Regulation of ribosomal protein genes: An ordered anarchy.Wiley interdisciplinary reviews. RNA · 2021Review
- Systematic analysis of bypass suppression of essential genes.Molecular systems biology · 2020Article
- Promoter Architecture and Promoter Engineering inMetabolites · 2020Review
- Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability.Molecular systems biology · 2020Article
- Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells.Nature communications · 2019Article
- Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis).BMC plant biology · 2019Article
- Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules.Scientific reports · 2019Article
47 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present single-molecule sequencing digital gene expression (smsDGE), a high-throughput, amplification-free method for accurate quantification of the full range of cellular polyadenylated RNA transcripts using a Helicos Genetic Analysis system. smsDGE involves a reverse-transcription and polyA-tailing sample preparation procedure followed by sequencing that generates a single read per transcript. We applied smsDGE to the transcriptome of Saccharomyces cerevisiae strain DBY746, using 6 of the available 50 channels in a single sequencing run, yielding on average 12 million aligned reads per channel. Using spiked-in RNA, accurate quantitative measurements were obtained over four orders of magnitude. High correlation was demonstrated across independent flow-cell channels, instrument runs and sample preparations. Transcript counting in smsDGE is highly efficient due to the representation of each transcript molecule by a single read. This efficiency, coupled with the high throughput enabled by the single-molecule sequencing platform, provides an alternative method for expression profiling.
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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.