Open Access Research article

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

Xiaojie Sun1, Shuqi Mei2, Hu Tao1, Guodong Wang1, Lina Su1, Siwen Jiang1, Changyan Deng1, Yuanzhu Xiong1 and Fenge Li1*

Author Affiliations

1 Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China

2 Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Hubei Academy of Agriculture Science, Wuhan, 430064, PR China

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BMC Genomics 2011, 12:111  doi:10.1186/1471-2164-12-111

Published: 16 February 2011

Additional files

Additional file 1:

Ovarian follicle transcriptome analyses using the Affymetrix Porcine Genechip. Data of each probe is from the three Large White sows (1, 2, 3) and three Chinese Taihu (1, 2, 3) sows. Raw data from. CEL files were converted to gene signal files and raw signals were normalized above to 500 on each array by MAS 5.0, and the dChip invariant set was used to normalize the signals of the different arrays. "P", present; "A", absent; "M", marginal; "Count (P)", the number of P flag; select while Count (P) ≥2 in two groups (Chen et al., 2009)*. Totally, 16,066 and 15,477 probesets were detected expression in the Large White and Taihu, respectively. *Chen H, Li C, Fang M, Zhu M, Li X, Zhou R, Li K, Zhao S. Understanding Haemophilus parasuis infection in porcine spleen through a transcriptomics approach. BMC Genomics. 2009, 5, 10:64.

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Additional file 2:

1476 transcripts that are differentially expressed in porcine ovary between Large White sows and Chinese Taihu sows (p ≤ 0.05). Totally 105 (row 5-109) transcripts have been annotated based on BLASTX searches. "FC", Fold change, gene expression level (normalized signal intensity) of Chinese Taihu sows compared to Large White sows, ">1" represents up regulation, "<1" represents down regulation. "p-value", significance level of differential expression for a particular gene by comparing their log 2 (normalized signal). "Gene name", top informative BLASTX hit.

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Additional file 3:

Pig unique genes (row 4-15), unique genes with BLSATX identity but no annotation (row 16-98) and unique genes with no BLASTX identity (row 99-136) (p ≤ 0.05, FC ≥ 2 or ≤ 0.5). "FC", Fold change, gene expression level (normalized signal intensity) of Chinese Taihu sows compared to Large White sows, "≥2" represents up regulation, "≤0.5" represents down regulation. "p-value", significance level of differential expression for a particular gene by comparing their log 2 (normalized signal). "Gene name", top informative BLASTX hit.

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Additional file 4:

Genes that distributed in the intervals of the known pig QTLs for reproduction traits. All the genes listed here are from 133 transcripts that are significantly up/down-regulated between Large White and Taihu sows. GenBank IDs represent annotated genes.

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Additional file 5:

Association between BAX and BMPR1B genotype and litter size traits. A and B, p ≤ 0.05; a and b, p = 0.09. ** p ≤ 0.05, *p ≤ 0.1 = 0.06. N: Number of investigated litters.

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Additional file 6:

Primer pairs designed for genes selected for validation by real time RT-PCR and SNP detection.

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