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Gene expression following treatment with HDAC6 inhibitor C1A

ABSTRACT: RNA Extraction from a human colon tumor developed in a xenograft mouse (Extraction from fresh frozen tumor tissue material). The affymetrix Human genome U219 array plate was used. Sequences used in the design of the array were selected from the Uingene database 219, RefSeq version 36, and full length human mRNAs from GenBank. Measure gene expression of more than 36 000 transcipts and variants per sample, which represent more than 20 000 genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE64662 | GEO | 2015/01/06

SECONDARY ACCESSION(S): PRJNA271588

REPOSITORIES: GEO

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Gene expression following treatment with HDAC6 inhibitor C1A

Project description:RNA Extraction from a human colon tumor developed in a xenograft mouse (Extraction from fresh frozen tumor tissue material). The affymetrix Human genome U219 array plate was used. Sequences used in the design of the array were selected from the Uingene database 219, RefSeq version 36, and full length human mRNAs from GenBank. Measure gene expression of more than 36 000 transcipts and variants per sample, which represent more than 20 000 genes. Study performed under contract by Alpha Metrix Biotech, Rodermark, Germany. Full details are available upon request. Processed data are available on the series record and consists of the differentially expressed genes identified in the comparison of the 14d_treated vs 24h_treated samples.

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Project description:The identification of new agents that may modulate the progression of cancer cell growth is of great interest. In this regard, dietary agents can be utilized to identify molecular targets to be used as part of a chemopreventive strategy. Walnuts contain several bioactive compounds, including pedunculagin, a polyphenol metabolized by microbiota to form urolithins, namely urolithin A (UA). We performed a genomic analysis to study the effect of UA on androgen-dependent LNCaP prostate adenocarcinoma cells. Cells were incubated with 40ÂµM UA for 24 hours, then, RNA was extracted. RNA samples were processed in the automated Biomek FX System (Beckman Coulter), where aRNA was produced, and labeled with Biotin, purified , fragmented and hybridized onto HG U219-24 Array, using the GeneChip HT 3âIVT Express Kit . Afterwards, the GeneTitanÂ® Multi-Channel (MC) Instrument (Affymetrix) was used to hybridize, wash , stain , and scan the arrays. Microarray results were analyzed using the GeneSpring GX v13.0 software. LNCaP cells were plated in 35mm wells, the following day they were treated with 40ÂµM urolithin A (UA) for 24 hours, after incubation Total RNA was extracted using Qiagen RNAeasy minikit. The Affymetrix Human Genome U219 array plate was used, which measures gene expression of more than 36 000 transcripts and variants per sample, which represent more than 20 000 genes.

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