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DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples.

Nielsen KL, Høgh AL, Emmersen J - Nucleic Acids Res. (2006)

Bottom Line: Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE).We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato.The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University DK-9000 Aalborg, Denmark.

ABSTRACT
Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato.

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Related in: MedlinePlus

Correlation of LongSAGE and DeepSAGE DOR tags (A) and DeepSAGE HAR (B). Data sets consisted of 51 918 LongSAGE tags, 122 100 DeepSAGE DOR tags and 91 580 DeepSAGE HAR tags. The most abundant DOR tag was encountered 1397 in LongSAGE and 3145 in DeepSAGE. The least abundant tags were seen once in all data sets. Using tags observed at least once in both libraries only (8567 tags) the R2 for the comparison of DOR Deep- and LongSAGE increase to 0.9694.
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fig3: Correlation of LongSAGE and DeepSAGE DOR tags (A) and DeepSAGE HAR (B). Data sets consisted of 51 918 LongSAGE tags, 122 100 DeepSAGE DOR tags and 91 580 DeepSAGE HAR tags. The most abundant DOR tag was encountered 1397 in LongSAGE and 3145 in DeepSAGE. The least abundant tags were seen once in all data sets. Using tags observed at least once in both libraries only (8567 tags) the R2 for the comparison of DOR Deep- and LongSAGE increase to 0.9694.

Mentions: Figure 3 shows a comparison of the numbers of LongSAGE DOR tags versus DeepSAGE DOR tags and DeepSAGE HAR tags, respectively. The distribution of DOR tags was very similar for the Long- and DeepSAGE methods (R2 = 0.96) showing that these measurements of the transcriptome are equivalent. Comparison of the transcriptomes at dormant and harvest were significantly different (R2 = 0.33) as expected. A similar correlation of R2 = 0.35 was obtained for DeepSAGE DOR versus DeepSAGE HAR (data not shown).


DeepSAGE--digital transcriptomics with high sensitivity, simple experimental protocol and multiplexing of samples.

Nielsen KL, Høgh AL, Emmersen J - Nucleic Acids Res. (2006)

Correlation of LongSAGE and DeepSAGE DOR tags (A) and DeepSAGE HAR (B). Data sets consisted of 51 918 LongSAGE tags, 122 100 DeepSAGE DOR tags and 91 580 DeepSAGE HAR tags. The most abundant DOR tag was encountered 1397 in LongSAGE and 3145 in DeepSAGE. The least abundant tags were seen once in all data sets. Using tags observed at least once in both libraries only (8567 tags) the R2 for the comparison of DOR Deep- and LongSAGE increase to 0.9694.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1636492&req=5

fig3: Correlation of LongSAGE and DeepSAGE DOR tags (A) and DeepSAGE HAR (B). Data sets consisted of 51 918 LongSAGE tags, 122 100 DeepSAGE DOR tags and 91 580 DeepSAGE HAR tags. The most abundant DOR tag was encountered 1397 in LongSAGE and 3145 in DeepSAGE. The least abundant tags were seen once in all data sets. Using tags observed at least once in both libraries only (8567 tags) the R2 for the comparison of DOR Deep- and LongSAGE increase to 0.9694.
Mentions: Figure 3 shows a comparison of the numbers of LongSAGE DOR tags versus DeepSAGE DOR tags and DeepSAGE HAR tags, respectively. The distribution of DOR tags was very similar for the Long- and DeepSAGE methods (R2 = 0.96) showing that these measurements of the transcriptome are equivalent. Comparison of the transcriptomes at dormant and harvest were significantly different (R2 = 0.33) as expected. A similar correlation of R2 = 0.35 was obtained for DeepSAGE DOR versus DeepSAGE HAR (data not shown).

Bottom Line: Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE).We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato.The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest.

View Article: PubMed Central - PubMed

Affiliation: Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University DK-9000 Aalborg, Denmark.

ABSTRACT
Digital transcriptomics with pyrophosphatase based ultra-high throughput DNA sequencing of di-tags provides high sensitivity and cost-effective gene expression profiling. Sample preparation and handling are greatly simplified compared to Serial Analysis of Gene Expression (SAGE). We compare DeepSAGE and LongSAGE data and demonstrate greater power of detection and multiplexing of samples derived from potato. The transcript analysis revealed a great abundance of up-regulated potato transcripts associated with stress in dormant potatoes compared to harvest. Importantly, many transcripts were detected that cannot be matched to known genes, but is likely to be part of the abiotic stress-response in potato.

Show MeSH
Related in: MedlinePlus