E-GEOD-5571 - Comparison of Gene Expression from Day 6 In Vivo- and In Vitro-Produced Porcine Blastocysts

Submitted on 21 August 2006, released on 23 August 2006, last updated on 10 June 2011
Sus scrofa
Samples (2)
Protocols (1)
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) 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.
Experiment type
transcription profiling by SAGE 
Jeremy R Miles <miles@email.marc.usda.gov>, C P Van Tassell, J R Miles, K A Zuelke, L A Blomberg, R E Everts, R L Krisher, T S Sonstegard
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-5571.idf.txt
Sample and data relationshipE-GEOD-5571.sdrf.txt
Processed data (1)E-GEOD-5571.processed.1.zip