Suitability of Stratagene reference RNA for analysis of lymphoid tissues

Karen Dybkær, Guimei Zhou, Javeed Iqbal, David Lee Kelly, Li Xiao, Simon Sherman, Francesco D'Amore, Wing C. Chan

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

We evaluated a lymphoid RNA standard prepared in our laboratory for spotted microarrays against the Universal Human Reference standard from Stratagene. Our goal was to determine if the Stratagene standard, which contains only two lymphoid cell lines out of a pool of 10 human cancer cell lines, had acceptable gene coverage to serve as a comprehensive standard for gene expression profiling of lymphoid tissues. Our lymphoid standard was prepared from thymus, spleen, tonsil, and cell lines representing immature B cells, plasma cells, and natural killer (NK) cells, thus covering the entire spectrum of lymphoid cells and most stromal elements present in specialized lymphoid tissues. The two standards were co-hybridized on oligonucleotide microarrays containing 17,260 genes, and both had fluorescence intensities above background for approximately 85% of the genes. Despite the limited representation of lymphoid cells in the Stratagene standard, only 4.2% genes exhibited expression differences greater than 2-fold including only 0.35% with differences greater than 4-fold. Although the lymphoid standard reflected a more comprehensive representation of immune system-associated genes, the Stratagene standard has the advantage of being commercially available, enabling easier comparison across laboratories and allowing comparative studies across a long period of time.

Original languageEnglish (US)
Pages (from-to)470-474
Number of pages5
JournalBioTechniques
Volume37
Issue number3
StatePublished - Sep 1 2004

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Lymphoid Tissue
RNA
Tissue
Cells
Genes
Lymphocytes
Microarrays
Gene expression
Cell Line
Thymus
B-Lymphoid Precursor Cells
Immune system
Palatine Tonsil
Gene Expression Profiling
Plasma Cells
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Natural Killer Cells
Thymus Gland
Immune System

ASJC Scopus subject areas

  • Biotechnology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Suitability of Stratagene reference RNA for analysis of lymphoid tissues. / Dybkær, Karen; Zhou, Guimei; Iqbal, Javeed; Kelly, David Lee; Xiao, Li; Sherman, Simon; D'Amore, Francesco; Chan, Wing C.

In: BioTechniques, Vol. 37, No. 3, 01.09.2004, p. 470-474.

Research output: Contribution to journalArticle

Dybkær, K, Zhou, G, Iqbal, J, Kelly, DL, Xiao, L, Sherman, S, D'Amore, F & Chan, WC 2004, 'Suitability of Stratagene reference RNA for analysis of lymphoid tissues', BioTechniques, vol. 37, no. 3, pp. 470-474.
Dybkær, Karen ; Zhou, Guimei ; Iqbal, Javeed ; Kelly, David Lee ; Xiao, Li ; Sherman, Simon ; D'Amore, Francesco ; Chan, Wing C. / Suitability of Stratagene reference RNA for analysis of lymphoid tissues. In: BioTechniques. 2004 ; Vol. 37, No. 3. pp. 470-474.
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