Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays

Daniel Bottomly, Nicole A R Walter, Jessica Ezzell Hunter, Priscila Darakjian, Sunita Kawane, Kari Buck, Robert Searles, Michael Mooney, Shannon McWeeney, Robert Hitzemann

Research output: Contribution to journalArticle

121 Citations (Scopus)

Abstract

C57BL/6J (B6) and DBA/2J (D2) are two of the most commonly used inbred mouse strains in neuroscience research. However, the only currently available mouse genome is based entirely on the B6 strain sequence. Subsequently, oligonucleotide microarray probes are based solely on this B6 reference sequence, making their application for gene expression profiling comparisons across mouse strains dubious due to their allelic sequence differences, including single nucleotide polymorphisms (SNPs). The emergence of next-generation sequencing (NGS) and the RNA-Seq application provides a clear alternative to oligonucleotide arrays for detecting differential gene expression without the problems inherent to hybridization-based technologies. Using RNA-Seq, an average of 22 million short sequencing reads were generated per sample for 21 samples (10 B6 and 11 D2), and these reads were aligned to the mouse reference genome, allowing 16,183 Ensembl genes to be queried in striatum for both strains. To determine differential expression, 'digital mRNA counting' is applied based on reads that map to exons. The current study compares RNA-Seq (Illumina GA IIx) with two microarray platforms (Illumina MouseRef-8 v2.0 and Affymetrix MOE 430 2.0) to detect differential striatal gene expression between the B6 and D2 inbred mouse strains. We show that by using stringent data processing requirements differential expression as determined by RNA-Seq is concordant with both the Affymetrix and Illumina platforms in more instances than it is concordant with only a single platform, and that instances of discordance with respect to direction of fold change were rare. Finally, we show that additional information is gained from RNA-Seq compared to hybridization-based techniques as RNA-Seq detects more genes than either microarray platform. The majority of genes differentially expressed in RNA-Seq were only detected as present in RNA-Seq, which is important for studies with smaller effect sizes where the sensitivity of hybridization-based techniques could bias interpretation.

Original languageEnglish (US)
Article numbere17820
JournalPLoS One
Volume6
Issue number3
DOIs
StatePublished - 2011

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Inbred DBA Mouse
Microarrays
Gene expression
RNA
Gene Expression
gene expression
mice
Genes
Inbred Strains Mice
hybridization
Oligonucleotide Array Sequence Analysis
oligonucleotides
Genome
RNA Sequence Analysis
Corpus Striatum
Oligonucleotide Probes
Gene Expression Profiling
neurophysiology
Neurosciences
genome

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. / Bottomly, Daniel; Walter, Nicole A R; Hunter, Jessica Ezzell; Darakjian, Priscila; Kawane, Sunita; Buck, Kari; Searles, Robert; Mooney, Michael; McWeeney, Shannon; Hitzemann, Robert.

In: PLoS One, Vol. 6, No. 3, e17820, 2011.

Research output: Contribution to journalArticle

Bottomly, Daniel ; Walter, Nicole A R ; Hunter, Jessica Ezzell ; Darakjian, Priscila ; Kawane, Sunita ; Buck, Kari ; Searles, Robert ; Mooney, Michael ; McWeeney, Shannon ; Hitzemann, Robert. / Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-Seq and microarrays. In: PLoS One. 2011 ; Vol. 6, No. 3.
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