A novel RNA sequencing data analysis method for cell line authentication

CCAT1 is an enhancer-templated RNA that predicts BET sensitivity in colorectal cancer

(2016) Mark L. McCleland et al.   JOURNAL OF CLINICAL INVESTIGATION

Authentication: A Standard Problem or a Problem of Standards?

(2016) Amanda Capes-Davis et al.   PLOS BIOLOGY

Standards for Cell Line Authentication and Beyond

(2016) Jamie L. Almeida et al.   PLOS BIOLOGY

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

A resource for cell line authentication, annotation and quality control

(2015) Mamie Yu et al.   NATURE

Reproducibility: changing the policies and culture of cell line authentication

(2015) Leonard P Freedman et al.   NATURE METHODS

Assessing the prevalence of mycoplasma contamination in cell culture via a survey of NCBI's RNA-seq archive

(2015) Anthony O. Olarerin-George et al.   NUCLEIC ACIDS RESEARCH

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

Comprehensive High-Throughput RNA Sequencing Analysis Reveals Contamination of Multiple Nasopharyngeal Carcinoma Cell Lines with HeLa Cell Genomes

(2014) M. J. Strong et al.   JOURNAL OF VIROLOGY

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

(2014) Guorong Xu et al.   PLoS One

U-251 revisited: genetic drift and phenotypic consequences of long-term cultures of glioblastoma cells

(2014) Anja Torsvik et al.   Cancer Medicine

Reliable Identification of Genomic Variants from RNA-Seq Data

(2013) Robert Piskol et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Y. Liao et al.   BIOINFORMATICS

Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data

(2013) Emma M. Quinn et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Screening the human exome: a comparison of whole genome and whole transcriptome sequencing

(2012) Elizabeth T Cirulli et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Recommendation of short tandem repeat profiling for authenticating human cell lines, stem cells, and tissues

(2010) Rita Barallon et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-ANIMAL

Check your cultures! A list of cross-contaminated or misidentified cell lines

(2010) Amanda Capes-Davis et al.   INTERNATIONAL JOURNAL OF CANCER

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS