ArticleBMC genomics2003
Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.
Article in BMC genomics, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 139 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
139 citing papers in PubMed, 226 citations in OpenAlex.
- TheCells · 2025Article
- Transcriptome changes of fission yeast cells exposed to fumonisin B1 or co-cultured with Fusarium verticillioides.Applied microbiology and biotechnology · 2025Article
- The Cdc14 phosphatase, Clp1, does not affect genome expression.microPublication biology · 2024Article
- Genetic effects on molecular network states explain complex traits.Molecular systems biology · 2023Article
- Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast.Life science alliance · 2022Article
- Molecular and comparative genomic analyses reveal evolutionarily conserved and unique features of the Schizosaccharomyces japonicus mycelial growth and the underlying genomic changes.Current genetics · 2021Article
- A modified culture medium and hyphae isolation method can increase quality of the RNA extracted from mycelia of a dimorphic fungal species.Current genetics · 2021Article
- Implementation of dCas9-mediated CRISPRi in the fission yeast Schizosaccharomyces pombe.G3 (Bethesda, Md.) · 2021Article
- OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential.EMBO reports · 2021Article
- Repression of a large number of genes requires interplay between homologous recombination and HIRA.Nucleic acids research · 2021Article
- Article
- Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast.EMBO reports · 2020Article
- Article
- Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance.Molecular systems biology · 2020Article
- Condensin locates at transcriptional termination sites in mitosis, possibly releasing mitotic transcripts.Open biology · 2019Article
- A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe.BMC genomics · 2019Article
- Bub1 kinase- and H2A phosphorylation-independent regulation of Shugoshin proteins under glucose-restricted conditions.Scientific reports · 2019Article
- Phosphorylation of the RNA-binding protein Zfs1 modulates sexual differentiation in fission yeast.Journal of cell science · 2017Article
- Schizosaccharomyces pombe rsv1 Transcription Factor and its Putative Homologues Preserved their Functional Homology and are Evolutionarily Conserved.Current microbiology · 2017Article
- Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
79 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
9 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe genome of the fission yeast Schizosaccharomyces pombe has recently been sequenced, setting the stage for the post-genomic era of this increasingly popular model organism. We have built fission yeast microarrays, optimised protocols to improve array performance, and carried out experiments to assess various characteristics of microarrays.
resultsWe designed PCR primers to amplify specific probes (180-500 bp) for all known and predicted fission yeast genes, which are printed in duplicate onto separate regions of glass slides together with control elements (approximately 13,000 spots/slide). Fluorescence signal intensities depended on the size and intragenic position of the array elements, whereas the signal ratios were largely independent of element properties. Only the coding strand is covalently linked to the slides, and our array elements can discriminate transcriptional direction. The microarrays can distinguish sequences with up to 70% identity, above which cross-hybridisation contributes to the signal intensity. We tested the accuracy of signal ratios and measured the reproducibility of array data caused by biological and technical factors. Because the technical variability is lower, it is best to use samples prepared from independent biological experiments to obtain repeated measurements with swapping of fluorochromes to prevent dye bias. We also developed a script that discards unreliable data and performs a normalization to correct spatial artefacts.
conclusionsThis paper provides data for several microarray properties that are rarely measured. The results define critical parameters for microarray design and experiments and provide a framework to optimise and interpret array data. Our arrays give reproducible and accurate expression ratios with high sensitivity. The scripts for primer design and initial data processing as well as primer sequences and detailed protocols are available from our website.
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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.