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Series GSE44674 Query DataSets for GSE44674
Status Public on Sep 07, 2013
Title Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase [RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The comparative whole genome transcriptome effects of two similar pharmaceuticals, imig or vela, on a Gaucher disease mouse model, 9V/null, were evaluated by two commonly used platforms, mRNA-Seq and microarray. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection. The biological pathways were similar between two platforms. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process. Although the two biopharmaceuticals have a very similar structure and function, imig- and vela- treatment in the mice differentially affected disease-specific pathways indicating the action of the two drugs on the disease process in the visceral tissues of Gaucher mouse model differ significantly at the molecular level. This study provides a comprehensive comparison between the two platforms (mRNA-Seq and microarray) for gene expression analysis and addresses the contribution of the different methods involved in the analysis of such data. The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment
 
Overall design 9V/null mice (Gaucher mouse model) were injected weekly via tail vein with 60U/kg/wk of imig or vela for 8 wks. Control 9V/null mice were injected with same volume of saline. Wt mice were untreated. Age and strain matched mice were used for the study. Also, statistical methods, DESeq and edgeR for mRNA-Seq and Mixed Model ANOVA for microarray, were compared for differential gene expression detection. Cell growth and proliferation, cell cycle, heme metabolism, and mitochondrial dysfunction were the most altered functions associated with the disease process. The results also provide insights into the differential molecular effects of two similar biopharmaceuticals for Gaucher disease treatment.
 
Contributor(s) Dasgupta N, Oh S, Xu Y, Sun Y, Jia L, Keddache M, Grabowski GG
Citation(s) 24124461
Submission date Feb 26, 2013
Last update date Sep 11, 2019
Contact name nupur dasgupta
Phone 513-803-1768
Organization name Cincinnati Children's Hopital Medical Center
Street address 3333 Burnet Ave.
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (55)
GSM1088679 LUCZKO_replicate1
GSM1088680 LUCZKO_replicate2
GSM1088681 LUCZKO_replicate3
This SubSeries is part of SuperSeries:
GSE44675 Gaucher Disease: Transcriptome Analyses Using Microarray or mRNA Sequencing in a Mouse Model Treated with velaglucerase alfa or imiglucerase
Relations
SRA SRP018865
BioProject PRJNA192575

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE44674_DESeq_normalised_matrix_file_all_55_samples.txt.gz 6.3 Mb (ftp)(http) TXT
GSE44674_TKT-TMM-EDGER-NORM-55-SAMPLES.txt.gz 5.1 Mb (ftp)(http) TXT
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Processed data are available on Series record
Raw data are available in SRA

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