| Publications (PDF) |
Baumforth et al., 2008 (1780 KB)
Expression of the Epstein-Barr Virus-Encoded Epstein-Barr Virus Nuclear Antigen 1 in Hodgkin's Lymphoma Cells Mediates Up-Regulation of CCL20 and the Migration of Regulatory T Cells. Am. J. Pathol. 173:195-204.
Microdissections were performed on cryosections using the PALM laser microdissector. For microarray analysis (Affymetrix HG-U133 Plus 2.0 GeneChips), RNA was extracted from 150-200 Hodgkin Reed-Sternberg cells or from GCs. RNA was amplified in two rounds with the ExpressArt TRinucleotide mRNA amplification kit.
|
Campean et al., 2008 (570 KB)
Campean et al., 2008
Laser microdissection (MMI AG, Switzerland), and use of ExpressArt N-Carrier ("Pico RNA Care") for RNA isolation, followed by analysis on Affymetrix RAE230A Microarray GeneChip.
|
Su et al., 2008 (424 KB)
Lambda light chain revision in the human intestinal IgA response. J Immunol 181:1264-1271.
Laser microdissection (P.A.L.M. Microlaser Technologies), and use of ExpressArt N-Carrier ("Pico RNA Care") for RNA isolation, followed by analysis with RT-PCR.
|
Hu et al., 2008 (256 KB)
Exon-level expression profiling: a comprehensive transcriptome analysis for oral fluids. Clin. Chem. 54(5): 824-832.
Conclusion: "It is feasible to use [very small] samples containing fragmented RNAs to conduct high-resolution expression profiling with coverage of the entire transcriptome and to validate multiple targets from limited amounts."
Goal was the analysis of amplified salivary RNA with Affymetrix Exon Arrays with the challenges of small sample size (< 5 ng total human RNA) and severe RNA degradation. The standard Affymetrix protocol with rRNA removal with magnetic beads (requires >100 ng of intact RNA) and subsequent RNA amplification by random priming (no selectivity against rRNAs, and requires >100 ng RNA) was impossible.
AmpTec's universal mRNA-specific linear amplification strategy (ExpressArt TRinucleotide mRNA amplification kit) has overcome both limitations. It provides selection against rRNAs, thus rRNA removal is obsolete, and two amplification rounds are possible to provide the necessary amounts of amplified mRNAs for Exon arrays. Array results were validated by qPCR data and an expression phenotype (male/female) was correctly identified.
|
Yanai, Baugh et al., 2008 (345 KB)
Pairing of competitive and topologically distinct regulatory modules enhances patterned gene expression. Mol. Syst. Biol. 4:163.
Study of the embryonic development of Caenorhabditis elegans is hampered by the fact that a complete organism provides only ~ 200 picograms of total RNA. Whole-genome microarray analysis necessitates extensive mRNA amplification. Although a sophisticated version of the standard, Eberwine-based technology has been developed [Baugh et al. (2001), Quantitative analysis of mRNA amplification by in vitro transcription. Nucleic Acids Res. 29:E29.], a minimum of 10 pooled embryos was still required.
A modification of ExpressArt technology [now available as ExpressArt Pico mRNA amplification kit, #8399-A12] has enabled this large-scale study with sub-nanogram RNA amounts. The RNA from 10 embryos could be safely split in half to provide a back-up for further analyses.
"We used RNAi and time series, whole-genome microarray analyses to systematically perturb and characterize components of a Caenorhabditis elegans lineage-specific transcriptional regulatory network. These data are supported by selected reporter gene analyses and comprehensive yeast one-hybrid and promoter sequence analyses."
|
Cummings et al., 2008 (286 KB)
Sexual and social stimuli elicit rapid and contrasting genomic responses. Proc. R. Soc. B 275: 393-402.
An initial evaluation of ExpressArt technology was performed [Duftner et al., 2008] and here, ExpressArt is applied in a differential gene expression study.
"Here we examine preference behaviour of 58 female swordtails, Xiphophorus nigrensis, in four different social environments (attractive and unattractive males, females only, non-attractive males only and asocial conditions) followed by neural gene expression profiling. We used a brain-specific cDNA microarray to identify patterns of genomic response and candidate genes, followed by quantitative PCR (qPCR) examination of gene expression with variation in behaviour. Our microarray results revealed patterns of genomic response differing more between classes of social stimuli than between presence versus absence of stimuli. ..... The identification of stimulus- and behaviour-specific responses opens an exciting window into the molecular pathways associated with social behaviour and mechanisms that underlie sexual selection."
|
Duftner et al., 2008 (804 KB)
Efficacy of RNA amplification is dependent on sequence characteristics: implications for gene expression profiling using a cDNA microarray. Genomics 91: 108-117.
Detailed study on potential bias introduced by mRNA amplification with the ExpressArt Nano mRNA amplification kit, provides also a brief overview of the ExpressArt technology. ExpressArt technology was subsequently used in a differential gene expression study [Cummings et al., 2008].
Obtained yields: "Assuming that 1-5% of total RNA correspond to poly(A)+ RNA, the first round of amplification yielded an approximately 1000- to 4000-fold increase, while the second round yielded an approximately 200-fold increase of poly(A)+ equivalents. These amplification factors correlate well with the expected values given by the manufacturer of the amplification kit for 500 ng input material in both the first and the second round of amplification."
"We applied a T7 polymerase-based technique [ExpressArt] to amplify RNA from two tissues of a cichlid fish and compared expression levels of unamplified and amplified RNA on a cDNA microarray. Amplification bias was generally minor and comprised features that were lost (1.3%) or gained (2.5%) through amplification and features that were scored as regulated before but unregulated after amplification (4.2%) or vice versa (19.5%). We examined 10 sequence-specific properties and found that GC content, folding energy, hairpin length and number, and lengths of poly(A) and poly(T) stretches significantly affected RNA amplification. We conclude that, if RNA amplification is used in gene expression studies, preceding experiments controlling for amplification bias should be performed."
|
Birgersdotter et al., 2007 (725 KB)
Three-dimensional culturing of the Hodgkin lymphoma cell-line L1236 induces a HL tissue-like gene expression pattern. Leukemia and Lymphoma 48: 2042-2053.
"To overcome some limitations of in vitro established cell-line tumor models for Hodgkin lymphoma (HL), we explored whether culturing in a three-dimensional (3D) matrix could improve the quality of the model..... The gene expression profile of the 3D-cultured HL derived cell-line L1236 was compared with that of suspension-cultured (2D) L1236, as well as to the gene expression profile found in HL tumor samples.
To validate our results we also included a gene expression data set of laser captured Hodgkin- Reed-Sternberg (H-RS) cells..... Between 150 and 200 H-RS cells or nonmalignant cells were isolated.... Following RNA extraction, three rounds of linear T7-based mRNA amplification were performed using the ExpressArt system....
The gene expression profiles were analyzed using Affymetrix technology. We found that the 3D culture affected gene expression of an HL derived cell-line, inducing a more tumor-related expression profile."
|
Bose et al., 2007 (646 KB)
Down-regulation of ATM protein in HRS cells of nodular sclerosis Hodgkin's lymphoma in children occurs in the absence of ATM gene inactivation. J Pathol 213:329-336.
Microdissections were performed on cryosections using the Leica or PALM laser microdissector. For microarray analysis (Affymetrix HG-U133 Plus 2.0 GeneChips), RNA was extracted from 200-250 Hodgkin Reed-Sternberg cells and amplified in two rounds with the ExpressArt Nano mRNA amplification kit.
|
Eickhoff et al., 2007 (548 KB)
Host cell responses to Chlamydia pneumoniae in gamma-interferon-induced persistence overlap those of productive infection and are linked to genes involved in apoptosis, cell cycle and metabolism. Infection and Immunity 75: 2853-2863.
RNA was isolated from cultured HeLa cells, to compare expression profiles of persistently infected cells with those of mock-infected cells. The ExpressArt Micro mRNA amplification kit was used for subsequent analysis with Affymetrix HG-U133A GeneChips. A high level of technical reproducibility was found, and a set of nineteen differentially expressed genes were selected for qPCR analysis. Microarray data were confirmed for seventeen genes.
|
Elvidge, 2006 (1.1 MB)
Microarray expression technology: from start to finish. Pharmocogenomics 7: 123-134.
Technology Report: An overview of methods and platforms is presented, including ExpressArt mRNA amplification with its unique ability to perform up to 3 amplification rounds and using sub-nanogram RNA quantities, combined with adaptations for degraded RNAs. |
Wetzel et al., 2006 (325 KB)
Bone morphogenetic protein-7 expression and activity in the human adult normal kidney is predominantly localized to the distal nephron. Kidney Int. 70: 717-723.
Laser microdissection (MMI AG, Switzerland), and use of ExpressArt N-Carrier ("Pico RNA Care") for RNA isolation, followed by qPCR.
|
McLucas et al., 2006 (187 KB)
Global gene expression analysis of the effects of Vinblastine on endothelial cells, when eluted from a thermo-responsive polymer. J. Biomed. Mater. Res. A: 246-253.
Use of ExpressArt mRNA amplification kit (Nano version) with subsequent hybridisation to human 40K OciChip.
|
Reis et al., 2006 (322 MB)
Isolation of mouse neuritic mRNAs. J Mol Histol. 37: 79-86.
Laser microdissection and use of ExpressArt mRNA amplification kit (Pico version) to visualize isolated RNA.
|
Gomez-Mancilla et al., 2005 (0.47 MB)
Central Nervous System Drug Development: An Integrative Biomarker Approach toward Individualized Medicine. NeuroRx. 2: 683-695.
This review represents an effort to illustrate the integration of state of the art and emerging technologies in drug development supporting the path of individualized medicine.
Citation: "Today, ExpressArt mRNA amplification technology based on TRinucleotide primers allows the complete amplification of all mRNA fragments in severely degraded RNA samples and works very well with extremely low limits of input RNA amounts (picogram range)."
|
Okuducu et al., 2005 (1.48 MB)
Cellular retinoic acid-binding protein 2 is down-regulated in prostate cancer. Int. J. Oncol. 27: 1273-1282.
Laser microdissection, subsequent use of ExpressArt mRNA amplification kit (2 amplification rounds), followed by cDNA array hybridisation.
|
Zeng et al., 2005 (343 KB)
Transcription factor Gfi1 regulates self-renewal and engraftment of hematopoietic stem cells. EMBO J. 23: 4116-4125.
ExpressArt Carrier ("Pico RNA Care") for RNA isolation from FACS-sorted cells.
|
Note: To read and print above publications you need the free software program Adobe Reader.
If you don't have the software, you can download an
Adobe Reader for free.
|
