Home LiteratureArticle Details
PMID: 17028099 Published · ppublish English Comparative Study Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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

Nucleic acids research ·Vol. 34 ·No. 19 ·2006-00-00 ·Pages e133

Nielsen KL, Høgh AL, Emmersen J

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.

MeSH Terms
Diphosphates/chemistry Gene Expression Profiling/methods Gene Expression Regulation, Plant RNA, Messenger/analysis Sequence Analysis, DNA Sequence Tagged Sites Solanum tuberosum/genetics,metabolism
Chemicals
Diphosphates RNA, Messenger
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Nielsen Kåre L
Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University DK-9000 Aalborg, Denmark.
Høgh Annabeth Laursen
Emmersen Jeppe
References (21)
21 references, click to expand
  1. Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.
    Nat Biotechnol. 2000 Jun;18(6):630-4 PMID: 10835600
  2. The role of a zinc finger-containing glycine-rich RNA-binding protein during the cold adaptation process in Arabidopsis thaliana.
    Plant Cell Physiol. 2006 Jun;47(6):793-8 PMID: 16608866
  3. Signal transduction mechanisms in plants: an overview.
    Curr Sci. 2001 Jan 25;80(2):170-7 PMID: 12194182
  4. Arabidopsis proteins containing similarity to the universal stress protein domain of bacteria.
    Plant Physiol. 2003 Mar;131(3):1209-19 PMID: 12644671
  5. Robust-LongSAGE (RL-SAGE): a substantially improved LongSAGE method for gene discovery and transcriptome analysis.
    Plant Physiol. 2004 Mar;134(3):890-7 PMID: 15020752
  6. DNA chip-based expression profile analysis indicates involvement of the phosphatidylinositol signaling pathway in multiple plant responses to hormone and abiotic treatments.
    Cell Res. 2004 Feb;14(1):34-45 PMID: 15040888
  7. Correction of sequence-based artifacts in serial analysis of gene expression.
    Bioinformatics. 2004 May 22;20(8):1254-63 PMID: 14871862
  8. Plastidial alpha-glucan phosphorylase is not required for starch degradation in Arabidopsis leaves but has a role in the tolerance of abiotic stress.
    Plant Physiol. 2004 Jun;135(2):849-58 PMID: 15173560
  9. A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips.
    Genomics. 2004 Oct;84(4):631-6 PMID: 15475240
  10. A novel extracellular matrix protein from tomato associated with lignified secondary cell walls.
    Plant Cell. 1994 Aug;6(8):1035-47 PMID: 7919979
  11. Serial analysis of gene expression.
    Science. 1995 Oct 20;270(5235):484-7 PMID: 7570003
  12. The significance of digital gene expression profiles.
    Genome Res. 1997 Oct;7(10):986-95 PMID: 9331369
  13. Expression monitoring by hybridization to high-density oligonucleotide arrays.
    Nat Biotechnol. 1996 Dec;14(13):1675-80 PMID: 9634850
  14. Incidence of "quasi-ditags" in catalogs generated by Serial Analysis of Gene Expression (SAGE).
    BMC Bioinformatics. 2004 Oct 18;5:152 PMID: 15491492
  15. Salt stress enhances xylem development and expression of S-adenosyl-L-methionine synthase in lignifying tissues of tomato plants.
    Planta. 2004 Dec;220(2):278-85 PMID: 15322882
  16. Decoding Ca2+ signals in plants.
    CRC Crit Rev Plant Sci. 2004;23(1):1-11 PMID: 16044584
  17. Analyzing the potato abiotic stress transcriptome using expressed sequence tags.
    Genome. 2005 Aug;48(4):598-605 PMID: 16094426
  18. Genome sequencing in microfabricated high-density picolitre reactors.
    Nature. 2005 Sep 15;437(7057):376-80 PMID: 16056220
  19. Expression profiles of hot pepper (Capsicum annum) genes under cold stress conditions.
    J Biosci. 2005 Dec;30(5):657-67 PMID: 16388140
  20. SCARFACE encodes an ARF-GAP that is required for normal auxin efflux and vein patterning in Arabidopsis.
    Plant Cell. 2006 Jun;18(6):1396-411 PMID: 16698946
  21. Using the transcriptome to annotate the genome.
    Nat Biotechnol. 2002 May;20(5):508-12 PMID: 11981567
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
1362-4962
DOI
10.1093/nar/gkl714
Published
2006-00-00
Epub
2006-00-05
Pages
e133
Language
English
Region
England
NLM ID
0411011
PMCID
PMC1636492
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/gkl714 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2