Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Serial analysis of chromatin occupancy (SACO) of forskolin-induced mRNA vs. an inactive control in the rat PC12 cell pheochromocytoma cell line to identify CREB targets

ABSTRACT: PC12 cells (passage 22) were cultured at 5% CO2 in a 37 C incubator. The growth medium was DMEM (high glucose, Invitrogen) supplemented with 25mM HEPES, 10% FCS, 5% FBS and 1x Pen/Strep (Invitrogen). 1x10^6 cells were starved overnight in DMEM +25 mM HEPES and treated with 10 uM 1,9 dideoxy forskolin or forskolin for 60 min. The final DMSO concentration was 0.05%. Total RNA was purified using Trizol (Invitrogen) according to the manufacturer's protocol. An additional round of purification was conducted using Rneasy columns (Qiagen) according to the manufacturer's protocol. cRNA was synthesized and labeled according to standard Affymetrix protocols. 2 biological replicates for the forskolin and 1,9 dideoxy forskolin conditions were run on Affymetrix RAE230 A and B chips for a total of 8 hybridizations.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Soren Impey 

PROVIDER: E-GEOD-2071 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions.

Impey Soren S   McCorkle Sean R SR   Cha-Molstad Hyunjoo H   Dwyer Jami M JM   Yochum Gregory S GS   Boss Jeremy M JM   McWeeney Shannon S   Dunn John J JJ   Mandel Gail G   Goodman Richard H RH  

Cell 20041201 7

The CREB transcription factor regulates differentiation, survival, and synaptic plasticity. The complement of CREB targets responsible for these responses has not been identified, however. We developed a novel approach to identify CREB targets, termed serial analysis of chromatin occupancy (SACO), by combining chromatin immunoprecipitation (ChIP) with a modification of SAGE. Using a SACO library derived from rat PC12 cells, we identified approximately 41,000 genomic signature tags (GSTs) that ma  ...[more]

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