Research article
mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft
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* Corresponding author: Joseph G Hacia hacia@hsc.usc.edu
1 Pharmacyclics Inc., 995 East Arques Avenue, Sunnyvale, CA, 94085, USA
2 Department of Biochemistry and Molecular Biology, University of Southern California, 2250 Alcazar Street, IGM 240, Los Angeles, CA, 90089, USA
3 Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089, USA
BMC Genomics 2008, 9:521 doi:10.1186/1471-2164-9-521
Published: 3 November 2008Additional files
Additional file 1:
Analysis of mitochondrial-encoded RNA transcript levels in A549 and A549 ρ0 xenografts by quantitative RT-PCR. Mitochondrial-encoded RNA transcript levels in A549 and A549 ρ0 xenografts are quantified by RT-PCR.
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Additional file 2:
Processed gene expression scores for all microarray analyses. Gene expression scores for all microarray experiments described in this manuscript.
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Additional file 3:
Volcano plots for gene expression comparisons considered in this study. The relationships between fold changes and P-values for the gene expression comparisons made in this study are provided.
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Additional file 4:
Differentially expressed transcripts in A549 ρ0 and A549 cells grown in culture. Probe sets showing differential expression in cultured A549 ρ0 and A549 cells are provided.
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Additional file 5:
Gene Ontology analysis of transcripts that are differentially expressed in A549 ρ0 cells relative to parental A549 cells in culture. Functional categories of transcripts showing differential expression in cultured A549 ρ0 and A549 cells are provided.
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Additional file 6:
Analysis of HIF-1 responsive genes in A549 ρ0 and A549 cells. Gene expression profiles of HIF-1 responsive genes in A549 ρ0 and A549 cells are provided.
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Additional file 7:
Transcripts that are differentially expressed in A549 ρ0 and A549 cells grown in xenografts. Probe sets showing differential expression in A549 ρ0 and A549 xenografts are provided.
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Additional file 8:
Gene Ontology analysis of transcripts that are differentially expressed in A549 ρ0 cells relative to parental A549 cells in xenografts. Functional categories of transcripts showing differential expression in cultured A549 ρ0 and A549 xenografts are provided.
Format: PPT Size: 296KB Download file
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Additional file 9:
Differential expression in A549 xenografts and A549 cell cultures. Probe sets showing differential expression in A549 xenografts and A549 cell cultures are provided.
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Additional file 10:
Differential expression in A549 ρ0 xenografts and A549 ρ0 cell cultures. Probe sets showing differential expression in A549 ρ0xenografts and A549 ρ0 cell cultures are provided.
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Additional file 11:
Probe sets where 50% or more of the variance in gene expression profiles is influenced by mtDNA status. Probe sets where 50% or more of the variance in gene expression profiles is influenced by mtDNA status are provided.
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Additional file 12:
Gene Ontology analysis of down-regulated transcripts in ρ0 cells whose variance is strongly influenced by mtDNA status. Functional categories of down-regulated transcripts in ρ0 cells whose variance is strongly influenced by mtDNA status are provided.
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Additional file 13:
Probe sets where 90% or more of the variance in gene expression profiles is influenced by growth conditions. Probe sets where 90% or more of the variance in gene expression profiles is influenced by growth conditions are provided.
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Additional file 14:
Gene Ontology analysis of transcripts whose variance are strongly dependent upon growth conditions. Functional categories of transcripts whose variance are strongly dependent upon growth conditions are provided.
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Additional file 15:
KEGG analysis of differentially expressed genes in A549 ρ0 and A549 cells. Biological pathways containing differentially expressed genes in A549 ρ0 and A549 cells are provided.
Format: XLS Size: 19KB Download file
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