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Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra‐deep sequencing technologies

Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using... 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Molecular Reproduction & Development Wiley

Transcriptional profiling of day 12 porcine embryonic disc and trophectoderm samples using ultra‐deep sequencing technologies

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References (28)

Publisher
Wiley
Copyright
"Copyright © 2010 Wiley Subscription Services, Inc., A Wiley Company"
ISSN
1040-452X
eISSN
1098-2795
DOI
10.1002/mrd.21226
pmid
20722012
Publisher site
See Article on Publisher Site

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.

Journal

Molecular Reproduction & Development – Wiley

Published: Sep 1, 2010

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