NIST logo

Publication Citation: Synthetic spike-in standards for RNA-seq experiments

NIST Authors in Bold

Author(s): Marc L. Salit; Lichun Jiang; Felix Schlesinger,; Brian Oliver; Carrie Davis; Yu Zhang; Renhua Li; Thomas R. Gingeras;
Title: Synthetic spike-in standards for RNA-seq experiments
Published: September 01, 2011
Abstract: High-throughput sequencing of cDNA (RNA-seq) is a widely deployed transcriptome profiling and annotation technique, but questions about the performance of different protocols and platforms remain. We used a newly developed pool of 96 synthetic RNAs with various lengths, and GC content covering a 220 concentration range as spike-in controls to measure sensitivity, accuracy, and biases in RNA-seq experiments as well as to derive standard curves for quantifying the abun- dance of transcripts. We observed linearity between read density and RNA input over the entire detection range and excellent agreement between replicates, but we observed significantly larger imprecision than expected under pure Poisson sampling errors. We use the control RNAs to directly measure reproducible protocol-dependent biases due to GC content and transcript length as well as stereotypic heterogeneity in coverage across transcripts correlated with position relative to RNA termini and priming sequence bias. These effects lead to biased quantification for short transcripts and individual exons, which is a serious problem for measurements of isoform abundances, but that can partially be corrected using appropriate models of bias. By using the control RNAs, we derive limits for the discovery and detection of rare transcripts in RNA-seq experiments. By using data collected as part of the model organism and human Encyclopedia of DNA Elements projects (ENCODE and modENCODE), we demonstrate that external RNA controls are a useful resource for evaluating sensitivity and accuracy of RNA-seq experiments for transcriptome discovery and quantification. These quality metrics facilitate comparable analysis across different samples, protocols, and platforms.
Citation: Genome Research
Volume: 21
Issue: 9
Pages: pp. 1543 - 1551
Keywords: Gene Expression; RNA-Seq; External RNA Control Consortium; SRM 2374; Spike-in Control; DNA Sequencing; RNA Sequencing; Functional Genomics; ENCODE Project; Technical Artifacts
Research Areas: Bioscience & Health
PDF version: PDF Document Click here to retrieve PDF version of paper (2MB)