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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Ago2 associated gene transcripts in two Hodgkin lymphoma cell lines

ABSTRACT: The aim of the study is to identify miRNA targets in Hodgkin lymphoma cell lines. By immunoprecipitation of wild type Ago2, it is expected to pull down the Ago2 associated gene transcripts. Through microarray analysis, the Ago2 associated gene transcripts identified are expected to be miRNA targets. Keywords: Ribonucleoprotein Immunoprecipitation - Gene Chip (RIP-Chip) RNA isolated from the Ago2 immunoprecipitated (IP) fraction is hybridized against the RNA from total cell lysate (T) fraction. The experiment is performed in two independent Hodgkin lymphoma cell lines, L1236 and L428. In addition, RNA of flow through (FT) fraction of L1236 is hybridized against RNA of total cell lysate (T) fraction of L1236 to demonstrate the specificity/enrichment seen in the IP fraction and not in the FT fraction. All hybridizations is done with a dye swap design.

ORGANISM(S): Homo sapiens

SUBMITTER: Bart-Jan Kroesen

PROVIDER: E-GEOD-14409 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A high throughput experimental approach to identify miRNA targets in human cells.

Tan Lu Ping LP Seinen Erwin E Duns Gerben G de Jong Debora D Sibon Ody C M OC Poppema Sibrand S Kroesen Bart-Jan BJ Kok Klaas K van den Berg Anke A

Nucleic acids research 20090904 20

The study of human microRNAs is seriously hampered by the lack of proper tools allowing genome-wide identification of miRNA targets. We performed Ribonucleoprotein ImmunoPrecipitation-gene Chip (RIP-Chip) using antibodies against wild-type human Ago2 in untreated Hodgkin lymphoma (HL) cell lines. Ten to thirty percent of the gene transcripts from the genome were enriched in the Ago2-IP fraction of untreated cells, representing the HL miRNA-targetome. In silico analysis indicated that approximate ...[more]

PMID: 19734348

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