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| Status |
Public on Apr 12, 2011 |
| Title |
Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarray |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
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| Summary |
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.
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| Overall design |
There are 5 male and 5 female C57BL/6J animals and 5 male and 5 female DBA/2J. These are adult, naïve animals. One array is run for each animal for a total of 20 Mouse MOE430 2.0 arrays. The purpose is to determine baseline (naïve) gene expression differences in striatum for these two inbred strains.
There are 12 male C57BL/6J animals and 12 male DBA/2J. These are adult, naïve animals. One array is run for each animal for a total of 24 Mouse Ref8 v2 arrays. The purpose is to determine baseline (naïve) gene expression differences in striatum for these two inbred strains.
***This submission represents the microarray component of the study
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| Contributor(s) |
Walter NA, Bottomly D, Hunter JE, Darakjian P, Kawane S, Buck KJ, Searles RP, Mooney M, McWeeney SK, Hitzemann R |
| Citation(s) |
21455293 |
| Submission date |
Dec 13, 2010 |
| Last update date |
Feb 11, 2019 |
| Contact name |
Nicole Walter |
| E-mail(s) |
waltern@ohsu.edu
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| Organization name |
Oregon Health & Science University
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| Department |
Behavioral Neuroscience
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| Lab |
Grant Lab
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| Street address |
3181 SW Sam Jackson Park Road
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239 |
| Country |
USA |
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| Platforms (2) |
| GPL1261 |
[Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array |
| GPL6885 |
Illumina MouseRef-8 v2.0 expression beadchip |
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| Samples (44)
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| Relations |
| BioProject |
PRJNA135487 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE26024_RAW.tar |
126.2 Mb |
(http)(custom) |
TAR (of CEL) |
| GSE26024_illumina_non-normalized.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSE26024_illumina_normalized.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
| Processed data are available on Series record |
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