SMARTer Stranded RNA-Seq Kit

cDNA libraries produced using the SMARTer Stranded RNA-Seq Kit show comparable yields and purity irrespective of input RNA concentrations

cDNA libraries produced using the SMARTer Stranded RNA-Seq Kit show comparable yields and purity irrespective of input RNA concentrations. Agilent 2100 Bioanalyzer gel-like image using a High Sensitivity DNA chip with cDNA libraries produced from between 100 ng–100 pg human brain polyA+ RNA with the number of PCR cycles indicated. cDNA libraries were produced by amplification with SeqAmp DNA Polymerase (included in the SMARTer Stranded RNA-Seq Kit).

The SMARTer Stranded RNA-Seq Kit provides high reproducibility and sensitivity over a thousand fold range of input RNA levels

The SMARTer Stranded RNA-Seq Kit provides high reproducibility and sensitivity over a thousand fold range of input RNA levels. Scatter plots of expression (FPKM) for cDNA libraries prepared from 100 ng and 100 pg of human brain polyA+ RNA show a high correlation, suggesting consistency across input levels. Axes are plotted on a log10 scale. Insets indicate the Pearson coefficient of correlation between replicates (R).

Data from technical replicates of each library indicate that the SMARTer Stranded RNA-Seq Kit delivers very consistent results across a wide range of input RNA concentrations

Data from technical replicates of each library indicate that the SMARTer Stranded RNA-Seq Kit delivers very consistent results across a wide range of input RNA concentrations. Comparisons of pairs of cDNA library replicas created from 100 ng and 100 pg of input RNA show high reproducibility across a wide range of input RNA. Axes are plotted on a log10 scale. Insets indicate the Pearson coefficient of correlation between replicates (R).

Even at the lowest levels tested (100 pg polyA+ input RNA), the SMARTer Stranded RNA-Seq Kit was able to maintain high accuracy while detecting ~15,000 genes using strand-specific alignments

Even at the lowest levels tested (100 pg polyA+ input RNA), the SMARTer Stranded RNA-Seq Kit was able to maintain high accuracy while detecting ~15,000 genes using strand-specific alignments.

High reproducibility with the SMARTer Stranded RNA-Seq Kit, confirmed by ERCC analysis

High reproducibility with the SMARTer Stranded RNA-Seq Kit, confirmed by ERCC analysis. Reads mapping to the ERCC data set from the previous experiments were pooled together and the FPKM was plotted against relative transcript abundance. The complete set of 92 ERCC transcripts was identified, with a slope of 0.934 and R2 of 0.9725. Axes are plotted on a log2 scale.

Indexed cDNA libraries were prepared according to the SMARTer Stranded RNA-Seq Kit protocol using twelve indices, and sequenced on an Illumina HiSeq Platform with 2 x 100 bp paired end reads

Indexed cDNA libraries were prepared according to the SMARTer Stranded RNA-Seq Kit protocol using twelve indices, and sequenced on an Illumina® HiSeq® Platform with 2 x 100 bp paired end reads. Short, overlapping reads originating from different strands of the genomic DNA were distinguished from each other, enabling quantitative expression analysis and accurate genome annotation. 99 of RNA-Seq reads mapped to the correct strand.

RiboGone – Mammalian removes rRNA efficiently from intact and degraded RNA, while retaining noncoding transcripts for analysis

RiboGone – Mammalian removes rRNA efficiently from intact and degraded RNA, while retaining noncoding transcripts for analysis. RNA-seq libraries were generated from Human Brain Total RNA (Clontech) or Breast Cancer FFPE RNA (Cureline, extracted using a NucleoSpin totalRNA FFPE kit) and treated with the indicated rRNA removal method. Reads were mapped to the hg19 genome and read distributions were determined using Picard RNA-Seq Metrics. Libraries generated from RiboGone-treated RNA had comparably low rRNA reads to oligo(dT)-enriched RNA (Clontech), while retaining more noncoding reads.