Differential Gene Expression in the Murine Thymus Assayed by Quantitative Hybridization of Arrayed cDNA Clones

Nguyen, Catherine; Rocha, Dominique; Granjeaud, Samuel; Baldit, Mylène; Bernard, Karine; Naquet, Philippe; Jordan, Bertrand

doi:10.1006/geno.1995.1233

Cited by 176 publications

(106 citation statements)

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“…Expression values obtained using DNA array hybridization are quantitative providing the experiments are done in a highly controlled way, as shown by ourselves (Nguyen et al, 1995;Bernard et al, 1996) and by others using di erent implementations of this method (Schena et al, 1995;Lockhart et al, 1996). This involves two distinct aspects: hybridization conditions ensuring large target excess, linear hybridization kinetics and uniform reaction rates across the array on the one hand, and detection methods providing linearity over a wide range on the other hand.…”

Section: Resultsmentioning

confidence: 99%

“…In both cases, the data were corrected for the amount of DNA in each spot as determined by vector oligonucleotide hybridization prior to complex probe hybridization. Details on genes, experimental procedures and data handling can be found in Nguyen et al (1995), Bernard et al (1996), Granjeaud et al (1996), Rocha et al (1997), and on our web site http: //tagc.univ-mrs.fr/pub/Cancer/ Figure 2 Di erential gene expression between two samples. (a) Top: membrane images after hybridization with complex probes made from total RNA from MDA-MB-134 mammary carcinoma (left) and Kato III gastric carcinoma (right) cell lines.…”

Section: Membranes and Obtention Of Hybridization Signaturesmentioning

confidence: 99%

“…The pT7T3D vector and poly(A) sequences (C3: 50-bp long, A10: 60-bp long, E6: 90-bp long) were used as negative controls; their signal determined the level of membrane background and checked for the elimination of spurious hybridization via the poly(A) tail present in some clones (Gress et al, 1992;Nguyen et al, 1995). We used a large excess (8 mg) of oligo(dT) primers (dT25) during the preparation of the complex probe and, at the end of the procedure, performed annealing of the labeled probe with poly(dA80).…”

Section: Membranes and Obtention Of Hybridization Signaturesmentioning

confidence: 99%

“…The approach using macroarrays in which PCR products from cDNAs are arranged on Nylon membranes and hybridized with radioactive probes (Nguyen et al, 1995;Bernard et al, 1996) is compatible with existing laboratory methods and equipment. A number of manufacturers have recognized this opportunity and provide ready-made macroarrays that can be quite useful.…”

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confidence: 99%

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Expression scanning of an array of growth control genes in human tumor cell lines

et al. 1999

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Analysis of gene expression on a medium-or large-scale is an increasingly recognized method for functional and clinical investigations based on the now extensive catalog of known or partially sequenced genes. The accessibility of this approach can be enhanced by using readily available technology (macroarrays on Nylon, radioactive detection) and the IMAGE resource to assemble sets of targets. We have set up such a medium-scale,¯exible system and validated it by the study of quantitative expression levels for 120 genes in six cell lines, including three mammary carcinoma cell lines. A number of important parameters are identi®ed as necessary for the assembly of a valid set and the obtention of goodquality quantitative data. The extensive data assembled in this survey identi®ed potential targets of carcinogenesis, for example the CRABP2 and GATA3 transcription factor genes. We also demonstrate the feasibility of this procedure for relatively small tumor samples, without recourse to probe ampli®cation methods.Keywords: cancer; breast cancer; gene expression; cDNA; gene array Recent studies have addressed the problem of alterations in human cancers in a global way, enumerating all genomic alterations, such as ampli®cations (Courjal et al

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Section: Resultsmentioning

confidence: 99%

Section: Membranes and Obtention Of Hybridization Signaturesmentioning

confidence: 99%

Section: Membranes and Obtention Of Hybridization Signaturesmentioning

confidence: 99%

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confidence: 99%

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Expression scanning of an array of growth control genes in human tumor cell lines

et al. 1999

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“…Thus, in the same experiment, genes expressed only in normal tissues (e.g., tumor suppressor genes), as well as genes that are tumor specific (e.g., tumor markers, activated oncogenes), can be identified [17].…”

Section: Identification Of the Genes Differentially Expressedmentioning

confidence: 99%

Downregulation of putative tumor suppressor gene TSC‐22 in human brain tumors

Shostak

Dmitrenko

Garifulin

et al. 2002

Journal of Surgical Oncology

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Background and Objectives: Our objective was to identify differentially expressed genes involved in the pathogenesis of glioblastoma multiforme (GBM). Methods: Screening of arrayed human fetal brain and human postnatal brain cDNA libraries was performed by differential hybridization with glioblastoma multiforme and human normal brain cDNAs. Results: Repeated differential hybridization of more than 100 cDNA clones selected by primary screening and analysis of RNA from adult normal brain and glial tumors showed 16 nucleotide sequences differentially expressed between normal brain and brain tumors. Among others, decreased content in astrocytic tumors was determined for TSC-22 mRNA corresponding to cDNA in the ICRFp507J1041 clone from human fetal brain cDNA library. Northern blot hybridization of RNA from different human brain tumors showed very low amounts of TSC-22 mRNA in most investigated samples of GBM, anaplastic astrocytoma, and some other tumors. Complete lack of expression of TSC-22 occurred in one sample of anaplastic astrocytoma, as well as in meningioma, brain sarcoma, sarcomatous meningioma, and oligodendroglioma. The differential expression of TSC-22 gene was confirmed by semiquantitative RT-PCR in 15 samples of astrocytomas WHO grade II-IV and three samples of normal brain. Conclusions: Significantly decreased levels of TSC-22 mRNA in human brain and salivary gland tumors and antiproliferative role of TSC-22 strongly suggest a tumor suppressor role for TSC-22.

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