Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Methylation profiling in various human cell lines and tissues by mDIP - methylated DNA precipitation with antibodies against methylated cytosine

ABSTRACT: Finding the methylation state of DNA promoters in various cell lines and tissues by mDIP - methylated DNA precipitation with antibodies against methylated cytosine.

INSTRUMENT(S): GenePix 4000B [Axon Instruments]

ORGANISM(S): Homo sapiens

DISEASE(S): primary tumor

SUBMITTER: Shlomit Farkash-Amar

PROVIDER: E-MEXP-520 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Evidence for an instructive mechanism of de novo methylation in cancer cells.

Keshet Ilana I Schlesinger Yeshayahu Y Farkash Shlomit S Rand Eyal E Hecht Merav M Segal Eran E Pikarski Eli E Young Richard A RA Niveleau Alain A Cedar Howard H Simon Itamar I

Nature genetics 20060201 2

DNA methylation has a role in the regulation of gene expression during normal mammalian development but can also mediate epigenetic silencing of CpG island genes in cancer and other diseases. Many individual genes (including tumor suppressors) have been shown to undergo de novo methylation in specific tumor types, but the biological logic inherent in this process is not understood. To decipher this mechanism, we have adopted a new approach for detecting CpG island DNA methylation that can be use ...[more]

PMID: 16444255

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Project description:Differentiated NT2 cells are a potentially useful model system to study herpes simples virus (HSV) replication in human neurons. These cells can be irreversibly differentiated into NT-neurons in the presence of retinoic acid and non-dividing cultures NT-neurons can be maintained for up to several months without retinoic acid. HSV is capable of infecting and replicating in differentiated NT-neurons and thus differentiated NT-neurons provide a ready source of human post-mitotic cells which can be useful to study certain aspects of the interaction of HSV and the neuron. Microarray analysis was used to examine how HSV-1 infection modulates cellular transcription in human NT-neurons, focusing on changes that take place during the first 24 hours following infection and compared to changes resulting from infection with inactivated virus. In addition, the transcriptional changes resulting from virus infection of neurons were compared to those observed in primary human fibroblasts. At early times after HSV infection a small number of cellular transcripts in NT-Neurons appear to be increased in abundance. Most of these transcripts that are up-regulated after infection are not unique to neuronal cells, and possibly represent a common cellular response to HSV infection. A few transcripts were not detected in infected human fibroblasts and may represent part of a transcriptional profile specific to this type of human neuronal cell. In contrast to the situation at early times after infection, analysis of cellular transcripts in NT-neurons at late times after infection is complicated by the overall profound decrease in cellular transcription. Thus, microarray analysis appeared to be most useful as a screening method for transcription changes following infection at early times after virus infection of NT-neurons. Two-condition experiment, HSV-1 infected versus uninfected fibroblasts, 3 independent biological replicate sets (uninfected/infected) in dual channel array setup (Cy3/Cy5).

Dataset Information

Methylation profiling in various human cell lines and tissues by mDIP - methylated DNA precipitation with antibodies against methylated cytosine

Publications

Evidence for an instructive mechanism of de novo methylation in cancer cells.

Similar Datasets

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