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Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra‐deep sequencing technologies
Author(s) -
Isom S. Clay,
Spollen William G.,
Blake Sean M.,
Bauer Bethany K.,
Springer Gordon K.,
Prather Randall S.
Publication year - 2010
Publication title -
molecular reproduction and development
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.745
H-Index - 105
eISSN - 1098-2795
pISSN - 1040-452X
DOI - 10.1002/mrd.21226
Subject(s) - biology , illumina dye sequencing , transcriptome , embryonic stem cell , deep sequencing , dna sequencing , genome , gene , gene expression profiling , genetics , embryo , computational biology , genomics , complementary dna , microbiology and biotechnology , gene expression
Abstract cDNA derived from trophectoderm (TE) and embryonic disc (ED) of a single day 12 porcine embryo was subjected to next‐generation sequencing using the Illumina platform. The short sequencing reads from triplicate sequencing runs were aligned to a custom database designed to represent the known porcine transcriptome. As expected, genes involved in epithelial cell function and steroid biosynthesis were more abundant in cells from the TE; genes involved in maintenance of pluripotency and chromatin remodeling were more highly expressed in cells from the ED. Quantitative real‐time PCR was used to confirm the validity of the approach. We conclude that gene expression profiles of even extremely small samples (≤1,000 cells) can be adequately described without RNA/cDNA preamplification. We also demonstrate the utility of pre‐genome genomics resources—such as EST repositories—in the analysis and application of next‐generation sequencing data in the absence of an appropriately annotated reference genome. Mol. Reprod. Dev. 77: 812–819, 2010. © 2010 Wiley‐Liss, Inc.