PMID- 21812063
OWN - NLM
STAT- MEDLINE
DCOM- 20120531
LR  - 20111118
IS  - 1098-2795 (Electronic)
IS  - 1040-452X (Linking)
VI  - 78
IP  - 9
DP  - 2011 Sep
TI  - Combining resources to obtain a comprehensive survey of the bovine embryo 
      transcriptome through deep sequencing and microarrays.
PG  - 651-64
LID - 10.1002/mrd.21364 [doi]
AB  - While most assisted reproductive technologies (ART) are considered routine for 
      the reproduction of species of economical importance, such as the bovine, the 
      impact of these manipulations on the developing embryo remains largely unknown. 
      In an effort to obtain a comprehensive survey of the bovine embryo transcriptome 
      and how it is modified by ART, resources were combined to design an 
      embryo-specific microarray. Close to one million high-quality reads were produced 
      from subtracted bovine embryo libraries using Roche 454 Titanium deep sequencing 
      technology, which enabled the creation of an augmented bovine genome catalog. 
      This catalog was enriched with bovine embryo transcripts, and included newly 
      discovered indel type and 3'UTR variants. Using this augmented bovine genome 
      catalog, the EmbryoGENE Bovine Microarray was designed and is composed of a total 
      of 42,242 probes, including 21,139 known reference genes; 9,322 probes for novel 
      transcribed regions (NTRs); 3,677 alternatively spliced exons; 3,353 3'-tiling 
      probes; and 3,723 controls. A suite of bioinformatics tools was also developed to 
      facilitate microrarray data analysis and database creation; it includes a quality 
      control module, a Laboratory Information Management System (LIMS) and microarray 
      analysis software. Results obtained during this study have already led to the 
      identification of differentially expressed blastocyst targets, NTRs, splice 
      variants of the indel type, and 3'UTR variants. We were able to confirm 
      microarray results by real-time PCR, indicating that the EmbryoGENE bovine 
      microarray has the power to detect physiologically relevant changes in gene 
      expression.
CI  - Copyright (c) 2011 Wiley-Liss, Inc.
FAU - Robert, Claude
AU  - Robert C
AD  - Laboratory of Functional Genomics of Early Embryonic Development, Universite 
      Laval, Quebec, Canada. claude.robert@fsaa.ulaval.ca
FAU - Nieminen, Julie
AU  - Nieminen J
FAU - Dufort, Isabelle
AU  - Dufort I
FAU - Gagne, Dominic
AU  - Gagne D
FAU - Grant, Jason R
AU  - Grant JR
FAU - Cagnone, Gael
AU  - Cagnone G
FAU - Plourde, Dany
AU  - Plourde D
FAU - Nivet, Anne-Laure
AU  - Nivet AL
FAU - Fournier, Eric
AU  - Fournier E
FAU - Paquet, Eric
AU  - Paquet E
FAU - Blazejczyk, Michal
AU  - Blazejczyk M
FAU - Rigault, Philippe
AU  - Rigault P
FAU - Juge, Nicolas
AU  - Juge N
FAU - Sirard, Marc-Andre
AU  - Sirard MA
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110802
PL  - United States
TA  - Mol Reprod Dev
JT  - Molecular reproduction and development
JID - 8903333
SB  - IM
MH  - Animals
MH  - Cattle/*embryology/*genetics
MH  - Computational Biology
MH  - Database Management Systems
MH  - Databases, Genetic
MH  - Embryo, Mammalian
MH  - Female
MH  - Gene Expression Profiling/*methods/standards
MH  - Granulosa Cells/metabolism
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Oligonucleotide Array Sequence Analysis/*methods
MH  - Real-Time Polymerase Chain Reaction
MH  - Reproducibility of Results
MH  - Reproductive Techniques, Assisted
MH  - Transcriptome/*physiology
MH  - User-Computer Interface
EDAT- 2011/08/04 06:00
MHDA- 2012/06/01 06:00
CRDT- 2011/08/04 06:00
PHST- 2011/03/21 00:00 [received]
PHST- 2011/07/08 00:00 [accepted]
PHST- 2011/08/04 06:00 [entrez]
PHST- 2011/08/04 06:00 [pubmed]
PHST- 2012/06/01 06:00 [medline]
AID - 10.1002/mrd.21364 [doi]
PST - ppublish
SO  - Mol Reprod Dev. 2011 Sep;78(9):651-64. doi: 10.1002/mrd.21364. Epub 2011 Aug 2.