A resource for transcriptomic analysis in the mouse brain

Charles Plessy, Michela Fagiolini, Akiko Wagatsuma, Norihiro Harasawa, Takenobu Kuji, Atsuko Asaka-Oba, Yukari Kanzaki, Sayaka Fujishima, Kazunori Waki, Hiroyuki Nakahara, Takao K. Hensch, Piero Carninci

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Background: 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. Methodology: 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. Conclusions: 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 expressed. Our clone collection will be a useful resource for the study of the transcriptome of single cell types in the cerebral cortex.

Original languageEnglish
Article numbere3012
JournalPloS one
Volume3
Issue number8
DOIs
Publication statusPublished - 2008 Aug 20
Externally publishedYes

ASJC Scopus subject areas

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

Fingerprint Dive into the research topics of 'A resource for transcriptomic analysis in the mouse brain'. Together they form a unique fingerprint.

  • Cite this

    Plessy, C., Fagiolini, M., Wagatsuma, A., Harasawa, N., Kuji, T., Asaka-Oba, A., Kanzaki, Y., Fujishima, S., Waki, K., Nakahara, H., Hensch, T. K., & Carninci, P. (2008). A resource for transcriptomic analysis in the mouse brain. PloS one, 3(8), [e3012]. https://doi.org/10.1371/journal.pone.0003012