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Results: 4

1.
Figure 1.

Figure 1. From: Digital transcriptome profiling from attomole-level RNA samples.

Attomole-level LQ-RNAseq methodology. Picogram-level RNA is reverse-transcribed with random primers and treated with RNase. Purified single-stranded first-strand cDNA is poly-A-tailed and 3′ blocked with terminal transferase. The poly-A-tailed cDNA is sequenced with the Helicos Genetic Analysis System.

Fatih Ozsolak, et al. Genome Res. 2010 April;20(4):519-525.
2.
Figure 2.

Figure 2. From: Digital transcriptome profiling from attomole-level RNA samples.

Reproducibility and quantitative ability of LQ-RNAseq. Reproducibility of S. cerevisiae polyA+ RNA (strain DBY746) expression profiles generated in two independent preparations of 250 pg of RNA run on different sequencers (A) and between 250-pg and 400-ng RNA preparations (B). (C,D) Comparison of LQ-RNAseq methodology to the published expression profile generated by oligo(dT) priming of 1 μg of polyA+ RNA from the same yeast strain used in this study (Lipson et al. 2009) (r = 0.915), and by random hexamer priming of 200 ng of RNA from another yeast strain (BY4741), adaptor ligation, and PCR amplification (Nagalakshmi et al. 2008) (r = 0.661). Log10 abundance is expressed using the number of unique reads aligned to each transcript in each sequencing experiment and expressed as reads number per kilobase per 1 million reads.

Fatih Ozsolak, et al. Genome Res. 2010 April;20(4):519-525.
3.
Figure 3.

Figure 3. From: Digital transcriptome profiling from attomole-level RNA samples.

Coverage of reads aligned in the + direction (A) and − direction (B) binned in 10-nt intervals is exemplified across the HTA1 gene (location: chr4 915,521–915,919; transcription direction: +). (C) Assignment of uniquely aligned S. cerevisiae polyA+ RNA reads to the categories shown. TSS (transcription start site) category refers to regions 200 nt upstream of annotated coding region start sites; 7.4% of reads map to the yeast TSS regions. Reads in the S. cerevisiae intergenic regions include reads aligning mostly to the potentially transcriptionally active transposon repeats. (D) Assignment of uniquely aligned human liver polyA+ RNA reads to the categories shown. TSS category refers to regions 200 nt upstream and downstream of the annotated RefSeq transcription start sites; 0.2% of the reads map to the human TSS regions. (E) Human liver polyA+ RNA reads uniquely aligning to human genome was binned at 50-nt intervals and visualized using the Integrated Genome Browser. Panel exemplifies the distribution of reads across the human CDO1 (location: chr5 115,168,329–115,180,304; transcription direction: −) gene's exonic (thick bars) and intronic (thin lines) regions. Y-axis indicates the number of reads per bin.

Fatih Ozsolak, et al. Genome Res. 2010 April;20(4):519-525.
4.
Figure 4.

Figure 4. From: Digital transcriptome profiling from attomole-level RNA samples.

Transcriptome profiling of B-iPS and ES cells. (A) Random hexamer and mNSR primer approaches using B-iPS RNA yield similar gene expression profiles. (B) Induced pluripotent stem cells derived from B lymphocytes exhibit expression profiles similar to embryonic stem cells. Log10 abundance is expressed using the number of unique reads aligned to each transcript in each sequencing experiment and is expressed as reads number per kilobase per 1 million reads. (C) Validation of differentially expressed genes identified by LQ-RNAseq with the qRT-PCR assay. (Black bars) Fold differences observed with LQ-RNAseq; (gray bars) fold differences observed with qRT-PCR. The two genes (Thoc1 and Rarg) exhibiting discrepant expression level changes may be due to the difference in the way expression levels are calculated with the two assays and the potential presence of alternative transcript isoforms.

Fatih Ozsolak, et al. Genome Res. 2010 April;20(4):519-525.

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