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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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Distribution of ditags length in LongSAGE (solid) and DeepSAGE (hatched).
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fig1: Distribution of ditags length in LongSAGE (solid) and DeepSAGE (hatched).

Mentions: A total of 224 310 sequences were obtained in a single sequence run, which included both forward and reverse sequences (Table 1). The distribution of the length between the two CATG sequences flanking the ditags (Figure 1) was found to be very similar to traditional LongSAGE. A PERL script (DeepSAGE_extract.pl) was used to extract 314 212 tags of 19 nt (167 367 from forward sequences and 146 845 from reverse sequences). Overall, 70% of these sequences yielded a good ditag sequence. This is comparable to our experience with traditional LongSAGE, where 73% of sequenced clones contained at least one ditag.


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

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

Distribution of ditags length in LongSAGE (solid) and DeepSAGE (hatched).
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Distribution of ditags length in LongSAGE (solid) and DeepSAGE (hatched).
Mentions: A total of 224 310 sequences were obtained in a single sequence run, which included both forward and reverse sequences (Table 1). The distribution of the length between the two CATG sequences flanking the ditags (Figure 1) was found to be very similar to traditional LongSAGE. A PERL script (DeepSAGE_extract.pl) was used to extract 314 212 tags of 19 nt (167 367 from forward sequences and 146 845 from reverse sequences). Overall, 70% of these sequences yielded a good ditag sequence. This is comparable to our experience with traditional LongSAGE, where 73% of sequenced clones contained at least one ditag.

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