Open Access Research article

Genome-wide differential gene expression in immortalized DF-1 chicken embryo fibroblast cell line

Byung-Whi Kong1*, Jeong Yoon Lee1, Walter G Bottje1, Kentu Lassiter1, Jonghyuk Lee2 and Douglas N Foster3

Author Affiliations

1 Department of Poultry Science, Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, Arkansas 72701, USA

2 Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA

3 Department of Animal Science, University of Minnesota, St. Paul, MN 55108, USA

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BMC Genomics 2011, 12:571  doi:10.1186/1471-2164-12-571

Published: 23 November 2011

Additional files

Additional file 1:

List of entire 3876 DE genes before sorting by IPA. The values indicate Log2 fold changes. The Agilent ID, gene symbol, gene name, GenBank accession numbers, chromosomal region, cytoband, GO ID, and oligo sequence on the array were provided.

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Additional file 2:

List of 902 DE genes identified by IPA database. The values indicate Log2 fold changes. The gene symbol, gene name, GenBank accession numbers, cellular locations, and molecule types were provided.

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Additional file 3:

List of focus molecules in gene networks. Gene symbols and GenBank accession numbers were displayed for the illustrations of network analysis. Only focus molecules, which were elected as differentially expressed genes from microarray analysis, include GenBank accession numbers, while accession numbers for reference molecules were not shown in the table.

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Additional file 4:

DF-1 cell growth responding to siRNA for E2F-1, BRCA1, and SRC. Each of four small siRNAs to target chE2F1 (A), chBRCA1 (B), chSRC (C), and chBeta-actin (D), in addition to a negative control siRNA were synthesized by Integrated DNA Technology Inc. (Coralville, IA). One million DF-1 cells were transfected with 300 pmole of each siRNA using Lipofectamine reagent (Invitrogen Life Technologies, Carlsbad, CA). Transfected cells were collected at 1 and 3 days post transfection (dpt), total cell numbers were counted, and the growth rates were determined by ratio of cell numbers at 3dpt and cell numbers at 1dpt. Results were compared to a negative control. Results of the most effective siRNA for each target were displayed. The siRNA for chBeta-actin was used as positive control to suppress DF-1 cell growth.

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Additional file 5:

DF-1 cell growth responding to 5-aza-2'-deoxycytidine treatment for the induction of p15INK4B. A 2 μM concentration of 5-aza-2'-deoxycytidine (5-aza), which is a demethylation chemical, was used to treat 1 million DF-1 cells, cells which were collected at 1, 2, 3, and 4 days post treatment. The mRNA expression of p15INK4B was determined by qRT-PCR at designated time points (A); cell morphology was visualized by phase-contrast microscopy (400 ×; B); and cell numbers were counted to determine growth rates (C).

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