RNA‐Seq‐based toxicogenomic assessment of fresh frozen and formalin‐fixed tissues yields similar mechanistic insights
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Summary
The results suggest that similar hypotheses about the biological mechanism of toxicity would be formulated from fresh frozen and FFPE samples, and indicate that phenotypically anchored archival specimens represent a potentially informative resource for signature‐based biomarker discovery and mechanistic characterization of toxicity.
- Type
- article
- Published
- 2015-07-01
- Cited by
- 26
- References
- 74
- OpenAlex
- https://openalex.org/W2119418029
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:12920691
Keywords
Transcriptome, Biology, Computational biology, RNA-Seq, Gene expression profiling
References
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Cited by
- Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues
- Intersection of toxicogenomics and high throughput screening in the Tox21 program: an NIEHS perspective
- High-mass-resolution MALDI mass spectrometry imaging of metabolites from formalin-fixed paraffin-embedded tissue
- Editor's Highlight: Dose-Response Analysis of RNA-Seq Profiles in Archival Formalin-Fixed Paraffin-Embedded Samples.
- Systems Biology for Organotypic Cell Cultures
- Robust detection of immune transcripts in FFPE samples using targeted RNA sequencing
- Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment
- A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples
- HAfTs are novel lncRNA transcripts from aflatoxin exposure
- Next generation sequencing data for use in risk assessment
- Transcriptomic points-of-departure from short-term exposure studies are protective of chronic effects for fish exposed to estrogenic chemicals.
- Mining the archives: a cross-platform analysis of gene expression profiles in archival formalin-fixed paraffin-embedded (FFPE) tissue
- A cross-sector call to improve carcinogenicity risk assessment through use of genomic methodologies
- Toxicity testing in the 21st century: progress in the past decade and future perspectives
- Using FFPE RNA-Seq with 12 marker genes to evaluate genotoxic and non-genotoxic rat hepatocarcinogens
- A Set of Six Gene Expression Biomarkers and Their Thresholds Identify Rat Liver Tumorigens in Short-Term Assays
- Sarcoma Molecular Pathological Diagnosis of FFPE Tissues without Dewaxing based on Lipidomic Profiles using SpiderMass Technology
- Wholistic approach: Transcriptomic analysis and beyond using archival material for molecular diagnosis
- Case study: Targeted RNA-sequencing of aged formalin-fixed paraffin-embedded samples for understanding chemical mode of action
- Pilot testing and optimization of a larval fathead minnow high throughput transcriptomics assay
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