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Series GSE9161 Query DataSets for GSE9161
Status Public on Jan 07, 2008
Title Expression profiling of cyclin D1 splice variants cyclin D1a and D1b in mouse 3T3 cells.
Organism Mus musculus
Experiment type Expression profiling by array
Summary Cyclin D1 is an important cell cycle regulator but in cancer its overexpression also increases cellular migration mediated by p27KIP1 stabilization and RhoA inhibition. Recently, a common polymorphism at the exon 4-intron 4 boundary of the human cyclin D1 gene within a splice donor region was associated with an altered risk of developing cancer. Altered RNA splicing caused by this polymorphism gives rise to a variant cyclin D1 isoform termed cyclin D1b, which has the same N-terminus as the canonical cyclin D1a isoform but a distinct C-terminus. Analysis was performed of mouse cyclin D1 knockout 3T3 cells infected with splice variants of cyclin D1. 3T3 cells transduced with retroviral vectors expressing each cyclin D1 isoform were processed for expression analysis.
Keywords: Cancer associated risk factor
Overall design Three Mouse Embryonic Fibroblasts cell lines obtained from littermate cyclin D1 knockout E14 embyos were serial passaged to obtain cyclin D1 knockout (D1KO) 3T3 cells. Each of the D1KO 3T3 cell lines were infected using the Murine Stem Cell Virus (MSCV) expressing splice variants of cyclin D1; cyclin D1a/ cyclin D1b or GFP control to give triplicate sample sets. 7 days post infection total RNA from each sample was extracted using Trizol and further purified using Qiagen’s RNeasy Kit. Preparation of biotinylated cRNA and hybridization to oligonucleotide arrays (Affymetrix mouse genome genechip 430 2.0) were performed in conjuction with Pestell lab and the Nucleic Acid Core Facility at Thomas Jefferson University. Mouse 430 2.0 genechip contains 39,000 transcripts. Gene chips were scanned and analyzed using Robust Multi-array Average (RMA) algorithm.
Contributor(s) Casimiro MC, Li Z, Wang C, Pestell RG
Citation(s) 18180298
Submission date Sep 25, 2007
Last update date Feb 11, 2019
Contact name Mathew Casimiro
Organization name Thomas Jefferson University
Department Cancer Biology
Lab Pestell Lab
Street address 1035 BLSB, 233 South 10th street
City Philadelphia
State/province PA
ZIP/Postal code 19107
Country USA
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (9)
GSM231384 Sample from retroviral MSCV-D1a infected cyclin D1 knockout 3T3 cells (line 1).
GSM231397 Sample from retroviral MSCV-D1b infected cyclin D1 knockout 3T3 cells (line 1).
GSM231405 Sample from retroviral MSCV-GFP control infected cyclin D1 knockout 3T3 cells (line 1).
BioProject PRJNA102715

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Supplementary file Size Download File type/resource
GSE9161_RAW.tar 32.9 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
Raw data provided as supplementary file

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