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Series GSE5571 Query DataSets for GSE5571
Status Public on Aug 23, 2006
Title Comparison of Gene Expression from Day 6 In Vivo- and In Vitro-Produced Porcine Blastocysts
Organism Sus scrofa
Experiment type Expression profiling by SAGE
Summary Production of embryos in vitro has enormous potential for research and commercial applications. Unfortunately, in vitro production of porcine embryos is extremely inefficient. Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development. The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE. Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries. Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively. A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively. Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively. Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs. Annotated tags were categorized into functional groupings according to gene ontology annotations. Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts. These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods.
Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos)
 
Overall design Whole-cell RNA from pools of Day 6 in vivo- and in vitro-produced blastocysts was used to construct small amplified RNA (SAR)-SAGE libraries.
 
Contributor(s) Miles JR, Blomberg LA, Krisher RL, Everts RE, Sonstegard TS, Van Tassell CP, Zuelke KA
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Submission date Aug 22, 2006
Last update date Mar 16, 2012
Contact name Jeremy R Miles
E-mail(s) miles@email.marc.usda.gov
Phone 402-762-4182
Organization name USDA-ARS
Street address State Spur 18A
City Clay Center
State/province NE
ZIP/Postal code 68933
Country USA
 
Platforms (1)
GPL1270 SAGE:10:NlaIII:Sus scrofa
Samples (2)
GSM129476 Day 6 in vivo-produced porcine blastocysts
GSM129478 Day 6 in vitro-produced porcine blastocysts
Relations
BioProject PRJNA95425

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