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Comparative Study
. 2006;34(19):e133.
doi: 10.1093/nar/gkl714. Epub 2006 Oct 5.

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

Kåre L Nielsen  1 , Annabeth Laursen Høgh, Jeppe Emmersen
Affiliations
Comparative Study

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

Kåre L Nielsen et al. Nucleic Acids Res. 2006.

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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Figures

Figure 1
Figure 1
Distribution of ditags length in LongSAGE (solid) and DeepSAGE (hatched).
Figure 2
Figure 2
Correlation of tag counts extracted from (A) forward and reverse sequences, respectively. Data sets consisted of 167 159 forward sequences and 199 413 reverse sequences. Using tags observed at least once in both directions only (12 025 tags) the R2 = 0.9611. (B) Counts extracted from two different sequencing runs. Data sets consisted of 96 427 tags from the first run and 26 673 tags from the second run. Using tags observed at least once in both runs only (6631 tags) the R2 = 0.9609.
Figure 3
Figure 3
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.
See this image and copyright information in PMC

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