Journal: BMC Genomics

Article Title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice

doi: 10.1186/s12864-015-1527-z

Figure Lengend Snippet: Comparing RNA-Seq and Agilent microarrays for detecting genes expressed in the liver and differentially expressed by TCDD. (A) RNA-Seq reads were aligned to mouse genome GRCm38 (release 74) and subsampled to represent 3–5 independent biological replicates. The number of differentially expressed genes (DEGs) was determined under varying |fold change| and P1( t ) criteria. (B) Microarray features were examined for DEGs under varying |fold change| and P1( t ) criteria. (C) RNA-Seq and microarray detected genes (yellow boxes) were examined for common and unique detected genes and DEGs. (D) Distribution of log 2 (fold change) and (E) P1( t ) values (P1 ( t ) ≥ 0) in RNA-Seq (blue) and Agilent (pink) datasets.

Article Snippet: Additional file 7: WaferGen SmartChip QRTPCR analysis of false-positive RNA-Seq genes.

Techniques: RNA Sequencing Assay, Microarray

Journal: BMC Genomics

Article Title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice

doi: 10.1186/s12864-015-1527-z

Figure Lengend Snippet: Effect of the number of independent biological replicates on RNA-Seq analysis. (A) DEGs were identified using a |fold change| ≥ 2.0 and P1( t ) ≥ 0.8 when examining 5 independent biological replicates or a subset of 3 or 4 replicates and compared for identified genes. Correlation of gene expression fold changes and P1( t ) values are illustrated comparing (B) 3 and 4, (C) 3 and 5, and (D) 4 and 5 biological replicates.

Article Snippet: Additional file 7: WaferGen SmartChip QRTPCR analysis of false-positive RNA-Seq genes.

Techniques: RNA Sequencing Assay, Expressing

Journal: BMC Genomics

Article Title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice

doi: 10.1186/s12864-015-1527-z

Figure Lengend Snippet: Comparison of RNA-Seq and Agilent DEGs. (A) Overlapping, RNA-Seq-specific and Agilent-specific DEGs were identified. Correlation of fold changes and P1( t ) values were examined for (B) all 12,165 expressed genes detected by both platforms, (C) the union of 1,722 differentially expressed genes (DEGs), and (D) the 449 DEGs detected by both platforms.

Article Snippet: Additional file 7: WaferGen SmartChip QRTPCR analysis of false-positive RNA-Seq genes.

Techniques: RNA Sequencing Assay

Journal: BMC Genomics

Article Title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice

doi: 10.1186/s12864-015-1527-z

Figure Lengend Snippet: Verification of RNA-Seq and Agilent DEG identification by WaferGen SmartChip Real-Time PCR analysis. (A) QRTPCR data (n = 5) was used as the “gold standard” to determine true and false positives and negatives for RNA-Seq (n = 3) and Agilent (n = 3) datasets. (B) Performance metrics of RNA-Seq and Agilent validated by QRTPCR. (C) Representative example of a false-negative and (D) false-positive response in the RNA-Seq dataset. Official gene symbols are indicated in upper left corner with the number of RNA-Seq aligned reads in parentheses () and number of samples with C t values lower than background in brackets [] for vehicle control samples. Bars represent mean fold-change determined by WaferGen technology (±SEM), the red line represents RNASeq fold-change, and the green line represents Agilent fold change. Significant differences within WaferGen data were determined by one-way ANOVA followed by Dunnett’s post-hoc test and indicated by an asterisk (*) with the exception of Fam83a whose undetectable levels prevented statistical testing. Red (RNA-Seq) and green (Agilent) dots represent P1 ( t ) values with size indicating level of significance (small ~0.8, large ~1). Labels on the X-axis indicate the dose of TCDD (μg/kg), number of aligned RNA-Seq reads, and number of samples with C t values lower than background. Dashed lines indicate 1.5 and 2.0 |fold-change| thresholds to identify DEGs. (E) UCSC genome browser track illustrating PCR primer and Agilent probe alignments for Zfp846. The Zfp846 loci is presented in blue with exons (closed boxes) and introns (solid line). The arrowheads indicate the direction of transcription.

Article Snippet: Additional file 7: WaferGen SmartChip QRTPCR analysis of false-positive RNA-Seq genes.

Techniques: RNA Sequencing Assay, Real-time Polymerase Chain Reaction

Journal: BMC Genomics

Article Title: RNA-Seq versus oligonucleotide array assessment of dose-dependent TCDD-elicited hepatic gene expression in mice

doi: 10.1186/s12864-015-1527-z

Figure Lengend Snippet: Comparison of RNA-Seq and Agilent dose–response modeling. (A) The ToxResponse modeler was used to identify genes fitting a sigmoidal response for the estimation of ED 50 s while (B) BMDExpress was used to find the best fit curves for point of departure (BMD and BMDL) estimates. Correlation of (C) ED 50 s and (D) BMD (blue circles) and BMDL (red circles) estimates were examined for all comparable genes.

Article Snippet: Additional file 7: WaferGen SmartChip QRTPCR analysis of false-positive RNA-Seq genes.

Techniques: RNA Sequencing Assay