Open Access Highly Accessed Research article

RNA-seq analysis of single bovine blastocysts

James L Chitwood1, Gonzalo Rincon1, German G Kaiser2, Juan F Medrano1 and Pablo J Ross1*

Author Affiliations

1 Department of Animal Science, University of California, Davis, 1 Shields Avenue, Davis, CA, USA

2 Laboratorio de Biotechnología de la Reproducción, INTA, Balcarce, Argentina

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BMC Genomics 2013, 14:350  doi:10.1186/1471-2164-14-350

Published: 25 May 2013

Additional files

Additional file 1: Figure S1:

Principal component analysis (PCA) of RPKM levels in single IVF blastocysts, pool of blastocysts from Huang and Khatib (2010) data, and milk somatic cells. Single and pool blastocyst datasets clustered close together while the somatic cells were further apart. This result supports the validity of single embryo RNA-seq analysis.

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Additional file 2: Figure S2:

Comparison of male vs. female embryo differential gene expression between RNA-seq and microarray results reported by Bermejo-Alvarez et al. 2010.

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Additional file 3: Figure S3:

The proportion of SNP validated by dbSNP as a proportion of the total detected was compared across coverage levels ranging from 4 to 30. Proportion validated increased moderately (approximately 7%) from 4 to 10, but this trend reached saturation at coverage of 14 (>55% validation). Minimum coverage for analysis was based on this saturation threshold.

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