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Series GSE5309 Query DataSets for GSE5309
Status Public on Jul 15, 2006
Title Transcriptional Profiling of Mammary Gland Side Population Cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary Similar to the bone marrow, the mammary gland contains a distinct population of Hoechst-effluxing side population cells, MG-SPs. To better characterize MG-SPs, their microarray gene profiles were compared to the remaining cells, which retain Hoechst dye (MG-NSPs). For analysis, gene ontology (GO) that describes genes in terms of biological processes and ontology traverser (OT) that performs enrichment analysis were utilized. OT showed that MG-SP specific genes were enriched in the GO categories of cell cycle regulation and checkpoints, multi-drug resistant transporters, organogenesis, and vasculogenesis. The MG-NSP upregulated genes were enriched in the GO category of cellular organization and biogenesis which includes basal epithelial markers, p63, smooth muscle actin (SMA), myosin, alpha-6 integrin, cytokeratin (CK) 14, as well as luminal markers, CK8 and CD24. Additional studies showed that a higher percentage of MG-SPs exist in the G1 phase of the cell cycle compared to the MG-NSPs. G1 cell cycle block of MG-SPs may be explained by higher expression of cell cycle negative regulatory genes such as TGF-beta2 (transforming growth factor-beta2), IGFBP-5 (insulin like growth factor binding protein-5), P18 INK4C and Wnt-5a (wingless-5a). Accordingly, a smaller percentage of MG-SPs expressed nuclear b-catenin, possibly as a consequence of the higher expression of Wnt-5a. In conclusion, microarray gene profiling suggests that MG-SPs are a lineage deficient mammary gland sub-population expressing key genes involved in cell cycle regulation, development and angiogenesis.

Supplemental File Descriptions:

Table 1 is a list of 1632 Genes differentially expressed by MG-SP and MG-NSP; Criteria for comparison included 1.2-fold difference in expression levels, false discovery rate (FDR) 9.4%, P value less than 0.05.

Table 2 is a list of 771 Genes differentially expressed by MG-SP and MG-NSP; Criteria for comparison included 1.5-fold difference in expression levels, FDR 3.4%, P value less than 0.05.

Table 3 is a list of 335 Genes differentially expressed by MG-SP and MG-NSP; Criteria for comparison included 2-fold difference in expression levels, FDR 0%, P value less than 0.05.

Table 4 is a list of 90 Genes differentially expressed by MG-SP and MG-NSP; Criteria for comparison included 2-fold difference in expression levels, FDR 0%, P value less than 0.01.

Keywords: Normal C57BL/6 Mammary Gland Epithelial Cells
Overall design Gene expression profiles were obtained by hybridizing amplified RNA from four replicate MG-SP and MG-NSP samples to Affymetrix 430 2.0 microarray chips. To isolate MG-SP and MG-NSPs, mammary gland cells were stained using the Hoechst dye 33342 and fluorescence displayed at two wavelength emissions, blue and red. The MG-SP and MG-NSP regions were indicated by trapezoids on the left (R1) and right (R2), respectively. We and others have previously shown that the R1 region is composed of side population cells since verapamil blocks their appearance. The cells in each region (R1 and R2) were sorted, their RNA isolated and amplified by two rounds of in vitro amplification and applied to Affymetrix chips. Hybridization, scanning, and production of raw data files were performed according to the Affymetrix standard protocols. Normalization and model-based expression measurements were performed with dChip. Two of the chips were eliminated from further analysis due to the high percentage of probe sets called an array outlier after model based expression analysis by dChip (Not included). The genes were filtered to eliminate those with very low expression values in most samples. From 45,000 probe sets, 16,744 probe sets were retained and used for further analysis. For normalization purposes and to allow for data comparison with other centers, universal mouse reference RNA (Stratagene) was hybridized to two chips. All other arrays were normalized to one of the universal mouse reference RNA arrays expressing average intensity closest to the median intensity of all chips (Stratagene Ref 2).
Contributor(s) Behbod F, Xian W, Shaw CA, Hilsenbeck SG, Anna T, Rosen JM
Citation(s) 16282442
Submission date Jul 13, 2006
Last update date Feb 11, 2019
Contact name Fariba Behbod
Phone 713-798-6211
Fax 713-798-8012
Organization name Baylor College of Medicine
Department Molecular and Cellular Biology
Lab Jeffrey M. Rosen
Street address One Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (7)
GSM120369 SP3 5-24-04 hnl_JR_865_MA2_3855.txt
GSM120370 NSP3 5-24-06 hnl_JR_865_MA2_3856.txt
GSM120371 SP4 6-14-04 hnl_JR_865_MA2_4113.txt
BioProject PRJNA96317

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Supplementary file Size Download File type/resource
GSE5309_RAW.tar 43.0 Mb (http)(custom) TAR (of CEL)
GSE5309_Table_1_CR_1632_Genes_1.2_fold_FDR_9.4percent.xls 1.0 Mb (ftp)(http) XLS
GSE5309_Table_2_CR_771_genes_1.5_fold_FDR_3.4percent.xls 765.5 Kb (ftp)(http) XLS
GSE5309_Table_3_CR_335_2_fold_FDR_0.xls 223.0 Kb (ftp)(http) XLS
GSE5309_Table_4_CR_90_genes_FDR_0_pless_than_0.01.xls 70.5 Kb (ftp)(http) XLS
Raw data provided as supplementary file

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