The impact of RNA extraction method on accurate RNA sequencing from formalin-fixed paraffin-embedded tissues

mRNA-seq whole transcriptome profiling of fresh frozen versus archived fixed tissues

(2018) Noa Bossel Ben-Moshe et al.   BMC GENOMICS

Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples

(2018) Isabella Wimmer et al.   Scientific Reports

Optimization of RNA Extraction from Formalin-Fixed Paraffin-Embedded Blocks for Targeted Next-Generation Sequencing

(2017) Yoojin Choi et al.   Journal of Breast Cancer

Molecular signatures in breast cancer

(2017) Samir Lal et al.   METHODS

A Comparison of RNA-Seq Results from Paired Formalin-Fixed Paraffin-Embedded and Fresh-Frozen Glioblastoma Tissue Samples

(2017) Anna Esteve-Codina et al.   PLoS One

Measure transcript integrity using RNA-seq data

(2016) Liguo Wang et al.   BMC BIOINFORMATICS

Translating RNA sequencing into clinical diagnostics: opportunities and challenges

(2016) Sara A. Byron et al.   NATURE REVIEWS GENETICS

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer

(2015) Deena M. A. Gendoo et al.   BIOINFORMATICS

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

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

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

Robust gene expression and mutation analyses of RNA-sequencing of formalin-fixed diagnostic tumor samples

(2015) Stefan Graw et al.   Scientific Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RNA-seq: impact of RNA degradation on transcript quantification

(2014) Irene Gallego Romero et al.   BMC BIOLOGY

Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

(2014) Debora Fumagalli 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

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

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Gene Expression, Single Nucleotide Variant and Fusion Transcript Discovery in Archival Material from Breast Tumors

(2013) Nadine Norton et al.   PLoS One

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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A New Molecular Predictor of Distant Recurrence in ER-Positive, HER2-Negative Breast Cancer Adds Independent Information to Conventional Clinical Risk Factors

(2011) Martin Filipits et al.   CLINICAL CANCER RESEARCH

Effects of Tissue Handling on RNA Integrity and Microarray Measurements From Resected Breast Cancers

(2011) Christos Hatzis et al.   JNCI-Journal of the National Cancer Institute

Genomic Index of Sensitivity to Endocrine Therapy for Breast Cancer

(2010) W. Fraser Symmans et al.   JOURNAL OF CLINICAL ONCOLOGY