Developments in microarray technologies

Howbrook, David N.; Valk, Anne M. van der; O'Shaughnessy, Meg C.; Sarker, Dipak K.; Baker, Susan C.; Lloyd, Andrew W.

doi:10.1016/s1359-6446(03)02773-9

Cited by 98 publications

(54 citation statements)

References 59 publications

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“…CodeLink TM is a microarray platform that allows the gene expression analysis of potentially thousands of transcriptomes using short oligonucleotide probes. CodeLink TM bioarrays are a well-established and powerful system that, in combination with bioinformatic tools (Bassett et al, 1999, Howbrook et al, 2003, Quackenbush, 2001, offers valuable insights into gene and molecular pathways involved in numerous biological events (Yoo et al, 2009). Gene expression microarrays have been used to discover genes that are differentially expressed in developmental processes (Hemberger et al, 2001, Kim et al, 2001, Tanaka et al, 2000.…”

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confidence: 99%

Genome-wide gene expression analysis in mouse embryonic stem cells

Sainz

García-Alcalde²,

Blanco³

et al. 2011

Int. J. Dev. Biol.

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Embryonic stem cell studies have generated great interest, due to their ability to form a wide variety of matured cells. However, there remains a poor understanding of mechanisms regulating the cell state of embryonic stem cells (ESCs) and of the genes they express during early differentiation. Gene expression analysis may be a valuable tool to elucidate either the molecular pathways involved in self-renewal and pluripotency, or early differentiation and to identify potential molecular therapy targets. The aim of this study was to characterize at the molecular level the undifferentiated mouse ESC state and the early development towards embryoid bodies. To attempt this issue, we performed CodeLink Mouse Uniset I 20K bioarrays in a well-characterized mouse ESC line, MES3, 3-and 7 day-old embryoid bodies and we compared our findings with those in adult tissue cells. Gene expression results were subsequently validated in a commercial stem cell line, CGR8 (ATCC). Significance Analysis of Microarrays (SAM) was used to identify statistically significant changes in microarray data. We identified 3664 genes expressed at significantly greater levels in MES3 stem cells than in adult tissue cells, which included 611 with 3-fold higher gene expression levels versus the adult cells. We also investigated the gene expression profile during early embryoid body formation, identifying 2040 and 2243 genes that were up-regulated in 3-and 7-day-old embryoid bodies, respectively. Our gene expression results in MES3 cells were partially confirmed in CGR8 cells, showing numerous genes that are expressed in both mouse stem cells. In conclusion, our results suggest that commonly expressed genes may be strong candidates for involvement in the maintenance of a pluripotent and undifferentiated phenotype and in early development. KEY WORDS: mouse stem cell line, gene expression profiling, early differentiationEmbryonic stem cell (ESC) research has provided a deeper understanding of cell development and is a promising area in medicine, but it is in a preliminary stage (Lagasse et al., 2001). Human ESCs have been used for a wide range of cell-based therapies, because they can potentially replace damaged cells in adult organisms (Korbling and Estrov, 2003). This replacement is possible because ESCs can propagate indefinitely in culture, maintaining a normal karyotype and undifferentiated state (Korbling and Estrov, 2003). This ability of ESCs to divide indefinitely provides an ideal system for the study of early development pathways and offers a potentially unlimited source of cells for organ transplantation and the development of novel therapies. In fact, therapies based on the use of human stem Int. J. Dev. Biol. 55: [995][996][997][998][999][1000][1001][1002][1003][1004][1005][1006] doi: 10.1387/ijdb.103123js www.intjdevbiol.com *Address correspondence to: Juan Sainz Pérez. Genomic Oncology area, Genyo -Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, 1st Floor, Office 4, Lab 6, Avda. d...

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confidence: 99%

Genome-wide gene expression analysis in mouse embryonic stem cells

Sainz

García-Alcalde²,

Blanco³

et al. 2011

Int. J. Dev. Biol.

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“…Conventional techniques for tumor analysis using whole-tissue sections are labour intensive and time consuming. The tissue microarray (TMA) technique was developed in 1998 for high-throughput analysis of multiple tumor samples in a single experiment and is now becoming an important tool for further investigation of information derived from DNA microarray studies (Kononen et al 1998 Howbrook et al 2003). TMA utilizes 0.6-mm core needle biopsies, which are obtained from archival paraffin-embedded tissue blocks and thereafter re-embedded in a novel paraffin array block.…”

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confidence: 99%

Experiences from tissue microarray in soft tissue sarcomas

Nilbert

Engellau

2004

Acta Orthopaedica Scandinavica

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“…Most microarray formats are of the size of a standard microscopic slide and can be easily handled. This allows the processing of many samples per assay and results in the generation of a high amount of data (Howbrook et al, 2003;Karakach et al, 2010). …”

Section: Principles Of Microarray Analysesmentioning

confidence: 99%