Mining the Archives: A Cross-Platform Analysis of Gene Expression Profiles in Archival Formalin-Fixed Paraffin-Embedded Tissues

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A Review of Preanalytical Factors Affecting Molecular, Protein, and Morphological Analysis of Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue: How Well Do You Know Your FFPE Specimen?

(2014) B. Paige Bass et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling

(2014) Wei Zhao et al.   BMC GENOMICS

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Next-Generation Sequencing of RNA and DNA Isolated from Paired Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Samples of Human Cancer and Normal Tissue

(2014) Jakob Hedegaard et al.   PLoS One

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens

(2013) David H. Spencer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Comparison of MicroRNA Deep Sequencing of Matched Formalin-Fixed Paraffin-Embedded and Fresh Frozen Cancer Tissues

(2013) Wei Meng et al.   PLoS One

Comparison of Microarrays and RNA-Seq for Gene Expression Analyses of Dose-Response Experiments

(2013) Michael B. Black et al.   TOXICOLOGICAL SCIENCES

Differential Expression of Long Noncoding RNAs in the Livers of Female B6C3F1 Mice Exposed to the Carcinogen Furan

(2013) Leslie Recio et al.   TOXICOLOGICAL SCIENCES

Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan

(2013) Anna Francina Jackson et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Preparation of archival formalin-fixed paraffin-embedded mouse liver samples for use with the Agilent gene expression microarray platform

(2013) A. Francina Jackson et al.   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Microarray Gene Expression Analysis of Fixed Archival Tissue Permits Molecular Classification and Identification of Potential Therapeutic Targets in Diffuse Large B-Cell Lymphoma

(2012) Kim Linton et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Furan in heat-treated foods: Formation, exposure, toxicity, and aspects of risk assessment

(2012) Sabrina Moro et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

(2011) Al Muktafi Sadi et al.   BMC CANCER

Genome-wide Gene Expression Profiling of Formalin-fixed Paraffin-Embedded Breast Cancer Core Biopsies Using Microarrays

(2011) Jan Budczies et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Ontology-Based Meta-Analysis of Global Collections of High-Throughput Public Data

(2010) Ilya Kupershmidt et al.   PLoS One

Application of Transcriptional Benchmark Dose Values in Quantitative Cancer and Noncancer Risk Assessment

(2010) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

Furan-induced dose–response relationships for liver cytotoxicity, cell proliferation, and tumorigenicity (furan-induced liver tumorigenicity)

(2008) Glenda J. Moser et al.   EXPERIMENTAL AND TOXICOLOGIC PATHOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

RNA expression analysis from formalin fixed paraffin embedded tissues

(2008) Susan M. Farragher et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Role of CYP2E1 in thioacetamide-induced mouse hepatotoxicity

(2007) Jin Seok Kang et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY