Open Access Research article

Transcriptome based identification of mouse cumulus cell markers that predict the developmental competence of their enclosed antral oocytes

Giulia Vigone1, Valeria Merico1, Alessandro Prigione2, Francesca Mulas3, Lucia Sacchi4, Matteo Gabetta4, Riccardo Bellazzi34, Carlo Alberto Redi1, Giuliano Mazzini5, James Adjaye26*, Silvia Garagna137* and Maurizio Zuccotti8*

Author Affiliations

1 Laboratorio di Biologia dello Sviluppo, Dipartimento di Biologia e Biotecnologie ‘Lazzaro Spallanzani’, Universita’ degli Studi di Pavia, Pavia, Italy

2 Department of Vertebrate Genomics. Max-Planck Institute for Molecular Genetics, Molecular Embryology and Aging Group, Berlin, Germany

3 Centro di Ingegneria Tissutale, Universita’ degli Studi di Pavia, Pavia, Italy

4 Dipartimento di Ingegneria Industriale e dell’Informazione, Universita’ degli Studi di Pavia, Pavia, Italy

5 Istituto di Genetica Molecolare – Consiglio Nazionale delle Ricerche, Via Ferrata 9, Pavia, Italy

6 Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany

7 Centro di Eccellenza in Biologia Applicata, Universita’ degli Studi di Pavia, Pavia, Italy

8 Dipartimento di Scienze Biomediche, Biotecnologiche e Traslazionali (S.Bi.Bi.T.), Sezione di Anatomia, Istologia ed Embriologia, Universita’ degli Studi di Parma, Via Volturno, Parma, 39-43125, Italy

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BMC Genomics 2013, 14:380  doi:10.1186/1471-2164-14-380

Published: 7 June 2013

Additional files

Additional file 1:

List of regulated genes. List of down- (green) and up- (red) regulated genes in the comparison between NSN-CCs vs. SN-CCs.

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Additional file 2:

Annotation-based gene networks. Node colours indicate the main GO biological process related to each gene, the size is adjusted proportionally to the Betweenness Centrality and increasing line width indicates stronger annotation relationship. (A) Pttg1 gene network made of 142 genes. (B) Pttg1 gene network made with its two more proximal neighbours.

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Additional file 3:

Interrogation of MeSH and STRING repositories. Genes belonging to the network originated from the analysis of the group of 247 regulated genes. Genes in green, down-regulated; genes in red, up-regulated.

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Additional file 4:

Lists of keywords related to folliculogenesis. MESH_B: set of basic key annotations. MESH_BC: initially selected key terms plus their child terms. MESH_BCP: initially selected key terms plus their parent terms.

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Additional file 5:

Bibliographic analysis. List of genes and their corresponding scores and p-values obtained for each set of key terms (MESH_B, MESH_BC, MESH_BCP) by means of the MeSH annotation analysis (see M&M). Results include the number of folliculogenesis key terms retrieved in the complete list of gene annotations (MESH), the number of key terms included in the most relevant terms (TFIDF), the value of the score that reflects the association of the gene to folliculogenesis keywords and its associated p-value (PVALUE_TFIDF). Numbers of terms rated as relevant by TFIDF (NUM_TFIDF) and retrieved articles (NUM_ARTICLES) are also indicated. In yellow, genes showing a p-value < 0.05 in all the three sets of key terms.

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Additional file 6:

Methods. MeSH annotation analysis.

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Additional file 7:

Primer sequences. List of primer sequences used for the qRT-PCR. F, forward primer; R, reverse primer.

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