Dataset Information

Quantitative assessment of transcriptome differences between brain territories.

ABSTRACT: Transcriptome analysis of mammalian brain structures is a potentially powerful approach in addressing the diversity of cerebral functions. Here, we used a microassay for serial analysis of gene expression (SAGE) to generate quantitative mRNA expression profiles of normal adult mouse striatum, nucleus accumbens, and somatosensory cortex. Comparison of these profiles revealed 135 transcripts heterogeneously distributed in the brain. Among them, a majority (78), although matching a registered sequence, are novel regional markers. To improve the anatomical resolution of our analysis, we performed in situ hybridization and observed unique expression patterns in discrete brain regions for a number of candidates. We assessed the distribution of the new markers in peripheral tissues using quantitative RT-PCR, Northern hybridization, and published SAGE data. In most cases, expression was higher in the brain than in peripheral tissues. Because the markers were selected according to their expression level, without reference to prior knowledge, our studies provide an unbiased, comprehensive molecular signature for various mammalian brain structures that can be used to investigate their plasticity under a variety of circumstances.

SUBMITTER: de Chaldee M

PROVIDER: S-EPMC403738 | biostudies-literature | 2003 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Quantitative assessment of transcriptome differences between brain territories.

de Chaldée Michel M Gaillard Marie-Claude MC Bizat Nicolas N Buhler Jean-Marie JM Manzoni Olivier O Bockaert Joël J Hantraye Philippe P Brouillet Emmanuel E Elalouf Jean-Marc JM

Genome research 20030701 7

Transcriptome analysis of mammalian brain structures is a potentially powerful approach in addressing the diversity of cerebral functions. Here, we used a microassay for serial analysis of gene expression (SAGE) to generate quantitative mRNA expression profiles of normal adult mouse striatum, nucleus accumbens, and somatosensory cortex. Comparison of these profiles revealed 135 transcripts heterogeneously distributed in the brain. Among them, a majority (78), although matching a registered seque ...[more]

PMID: 12840043

Similar Datasets

Project description:The simultaneous recording of brain activity in two or more people, termed hyperscanning, is an emerging field of research investigating the neural basis of social interaction. Hyperscanning studies of adult–infant dyads (e.g., parent and infant) have great potential to provide insights into how social functions develop. In particular, taking advantage of functional near-infrared spectroscopy (fNIRS) for its spatial resolution and invulnerability to motion artifacts, adult–infant fNIRS may play a major role in this field. However, there remains a problem in analyzing hyperscanning data between adult and young populations. Namely, there are intrinsic differences in hemodynamic time latencies depending on age, and the peak latency of the hemodynamic response function (HRF) is longer in younger populations. Despite this fact, the effects of such differences on quantified synchrony have not yet been examined. Consequently, the present study investigated the influence of intrinsic hemodynamic differences on wavelet coherence for assessing brain synchrony, and further examined the statistical removal of these effects through simulation experiments. First, we assumed a social signal model, where one counterpart of the dyad (e.g., infant) sends a social signal to the other (e.g., parent), which eventually results in simultaneous brain activation. Based on this model, simulated fNIRS activation sequences were synthesized by convolving boxcar event sequences with HRFs. We set two conditions for the event: synchronized and asynchronized event conditions. We also modeled the HRFs of adults and infants by referring to previous studies. After preprocessing with additional statistical processing, we calculated the wavelet coherence for each synthesized fNIRS activation sequence pair. The simulation results showed that the wavelet coherence in the synchronized event condition was attenuated for the combination of different HRFs. We also confirmed that prewhitening via an autoregressive filter could recover the attenuation of wavelet coherence in the 0.03–0.1 Hz frequency band, which was regarded as being associated with synchronous neural activity. Our results showed that variability in hemodynamics affected the analysis of inter-brain synchrony, and that the application of prewhitening is critical for such evaluations between adult and young populations.

Project description:BACKGROUND: Populus euphratica Oliv and P. pruinosa Schrenk (Salicaceae) both grow in dry desert areas with high summer temperatures. However, P. euphratica is distributed in dry deserts with deep underground water whereas P. pruinosa occurs in deserts in which there is underground water close to the surface. We therefore hypothesized that these two sister species may have evolved divergent regulatory and metabolic pathways during their interaction with different salt habitats and other stresses. To test this hypothesis, we compared transcriptomes from callus exposed to 24 h of salt stress and control callus samples from both species and identified differentially expressed genes (DEGs) and alternative splicing (AS) events that had occurred under salt stress. RESULTS: A total of 36,144 transcripts were identified and 1430 genes were found to be differentially expressed in at least one species in response to salt stress. Of these DEGs, 884 and 860 were identified in P. euphratica and P. pruinosa, respectively, while 314 DEGs were common to both species. On the basis of parametric analysis of gene set enrichment, GO enrichment in P. euphratica was found to be significantly different from that in P. pruinosa. Numerous genes involved in hormone biosynthesis, transporters and transcription factors showed clear differences between the two species in response to salt stress. We also identified 26,560 AS events which were mapped to 8380 poplar genomic loci from four libraries. GO enrichments for genes undergoing AS events in P. euphratica differed significantly from those in P. pruinosa. CONCLUSIONS: A number of salt-responsive genes in both P. euphratica and P. pruinosa were identified and candidate genes with potential roles in the salinity adaptation were proposed. Transcriptome comparisons of two sister desert poplar species under salt stress suggest that these two species may have developed different genetic pathways in order to adapt to different desert salt habitats. The DEGs that were found to be common to both species under salt stress may be especially important for future genetic improvement of cultivated poplars or other crops through transgenic approaches in order to increase tolerance of saline soil conditions.

Dataset Information

Quantitative assessment of transcriptome differences between brain territories.

Publications

Quantitative assessment of transcriptome differences between brain territories.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets