ArticleScientific reports2015
A high-throughput RNA-seq approach to profile transcriptional responses.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The trial behind it
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
13 citing papers in PubMed.
- Species-wide quantitative transcriptomes and proteomes reveal distinct genetic control of gene expression variation in yeast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Transcriptional Signatures and Network-Based Approaches Identified Master Regulators Transcription Factors Involved in Experimental Periodontitis Pathogenesis.International journal of molecular sciences · 2023Article
- MAC-Seq: Coupling Low-Cost, High-Throughput RNA-Seq with Image-Based Phenotypic Screening in 2D and 3D Cell Models.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Trends and Applications of Omics Technologies to Functional Characterisation of Enzymes and Protein Metabolites Produced by Fungi.Journal of fungi (Basel, Switzerland) · 2021Review
- Article
- Interpreting Coronary Artery Disease Risk Through Gene-Environment Interactions in Gene Regulation.Genetics · 2019Article
- Article
- Environmental influences on RNA processing: Biochemical, molecular and genetic regulators of cellular response.Wiley interdisciplinary reviews. RNA · 2019Review
- CD40 ligand deficiency causes functional defects of peripheral neutrophils that are improved by exogenous IFN-γ.The Journal of allergy and clinical immunology · 2018Article
- Environmental perturbations lead to extensive directional shifts in RNA processing.PLoS genetics · 2017Article
- RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes.Scientific reports · 2017Article
- High-throughput allele-specific expression across 250 environmental conditions.Genome research · 2016Article
- Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
In recent years RNA-seq protocols have been developed to investigate a variety of biological problems by measuring the abundance of different RNAs. Many study designs involve performing expensive preliminary studies to screen or optimize experimental conditions. Testing a large number of conditions in parallel may be more cost effective. For example, analyzing tissue/environment-specific gene expression generally implies screening a large number of cellular conditions and samples, without prior knowledge of which conditions are most informative (e.g., some cell types may not respond to certain treatments). To circumvent these challenges, we have established a new two-step high-throughput RNA-seq approach: the first step consists of gene expression screening of a large number of conditions, while the second step focuses on deep sequencing of the most relevant conditions (e.g., largest number of differentially expressed genes). This study design allows for a fast and economical screen in step one, with a more efficient allocation of resources for the deep sequencing of the most biologically relevant libraries in step two. We have applied this approach to study the response to 23 treatments in three lymphoblastoid cell lines demonstrating that it should also be useful for other high-throughput transcriptome profiling applications requiring iterative refinement or screening.
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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.