A resource for transcriptomic analysis in the mouse brain.

PloS One
Charles PlessyPiero Carninci

Abstract

The transcriptome of the cerebral cortex is remarkably homogeneous, with variations being stronger between individuals than between areas. It is thought that due to the presence of many distinct cell types, differences within one cell population will be averaged with the noise from others. Studies of sorted cells expressing the same transgene have shown that cell populations can be distinguished according to their transcriptional profile. We have prepared a low-redundancy set of 16,209 full-length cDNA clones which represents the transcriptome of the mouse visual cortex in its coding and non-coding aspects. Using an independent tag-based approach, CAGE, we confirmed the cortical expression of 72% of the clones. Clones were amplified by PCR and spotted on glass slides, and we interrogated the microarrays with RNA from flow-sorted fluorescent cells from the cerebral cortex of parvalbumin-egfp transgenic mice. We provide an annotated cDNA clone collection which is particularly suitable for transcriptomic analysis in the mouse brain. Spotting it on microarrays, we compared the transcriptome of EGFP positive and negative cells in a parvalbumin-egfp transgenic background and showed that more than 30% of clones are differentially expr...Continue Reading

References

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Sep 30, 2003·BioTechniques·Tomoko Hirozane-KishikawaPiero Carninci
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Citations

Nov 13, 2010·Science·Hirofumi MorishitaTakao K Hensch
Apr 28, 2012·BMC Genomics·Danielle HickfordMarilyn B Renfree
Jun 19, 2013·Cell Reports·Julien SpatazzaAlain Prochiantz
Jan 25, 2012·Cellular and Molecular Neurobiology·Ruby KwongMichal Janitz
Jun 7, 2012·BioTechniques·Alka SaxenaPiero Carninci

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Datasets Mentioned

BETA
GSE8968
GPL5681

Methods Mentioned

BETA
PCR
transgenic
dissection

Software Mentioned

LOWESS
craw
FANTOM3
QVALUE
fasta3
stackPACK
Acuity
d2
phrap
geneid

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