A resource for transcriptomic analysis in the mouse brain.
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.


METHODS
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.
Plessy
Charles
C
Functional Genomics Technology Team, Omics Science Center, RIKEN Yokohama Institute, Yokohama, Kanagawa, Japan.
Fagiolini
Michela
M
Wagatsuma
Akiko
A
Harasawa
Norihiro
N
Kuji
Takenobu
T
Asaka-Oba
Atsuko
A
Kanzaki
Yukari
Y
Fujishima
Sayaka
S
Waki
Kazunori
K
Nakahara
Hiroyuki
H
Hensch
Takao K
TK
Carninci
Piero
P
D000818:Animals; D001921:Brain / Q000502:physiology*; D002531:Cerebellum / Q000502:physiology; D018076:DNA, Complementary / Q000235:genetics; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D015723:Gene Library; D051379:Mice; D015233:Models, Statistical; D009419:Nerve Tissue Proteins / Q000235:genetics; D014158:Transcription, Genetic; D014793:Visual Cortex / Q000502:physiology*
D018076:DNA, Complementary; D009419:Nerve Tissue Proteins