Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

De novo assembly and annotation of the singing mouse genome

ABSTRACT: We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.

ORGANISM(S): Scotinomys teguina

PROVIDER: GSE212957 | GEO | 2023/08/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Weighted gene coexpression analysis of RNA-seq data from 65d juvenile Area X and adjacent non-song ventral striatopallidum (VSP).

Project description:Human speech is one of the few examples of vocal learning among mammals, yet ~half of avian species exhibit this ability. Its genetic basis is unknown beyond a shared requirement for FoxP2 in both humans and zebra finches. Here we manipulated FoxP2 isoforms in Area X during a critical period for song development, delineating, for the first time, unique contributions of each to vocal learning. We used weighted gene coexpression network analysis of RNA-seq data to construct transcriptional profiles and found gene modules correlated to singing, learning, or vocal variability. The juvenile song modules were preserved adults, whereas the learning modules were not. The learning modules were preserved in the striatopallidum adjacent to Area X whereas the song modules were not. The confluence of learning and singing coexpression in juvenile, but not adult, Area X may underscore molecular processes that drive vocal learning in zebra finches and, by analogy, humans.

2018-01-25 | GSE96843 | GEO

Weighted gene co-expression network analysis on microarray data from subregions of zebra finch (Taeniopygia guttata) basal ganglia

Project description:Similarities between speech and birdsong make songbirds advantageous for investigating the neurogenetics of learned vocal communication; a complex phenotype likely supported by ensembles of interacting genes in cortico-basal ganglia pathways of both species. To date, only FoxP2 has been identified as critical to both speech and birdsong. We performed weighted gene co-expression network analysis on microarray data from singing zebra finches to discover gene ensembles regulated during vocal behavior. We found ~2,000 singing- regulated genes comprising 3 co-expression groups unique to area X, the basal ganglia subregion dedicated to learned vocal-motor behavior. These contained known targets of human FOXP2 and potential avian targets. We validated novel biological pathways for vocalization. Our findings show that higher-order gene co-expression patterns, rather than expression levels, molecularly distinguish area X from the ventral striato-pallidum during singing. The previously unknown structure of singing-driven networks enables prioritization of molecular interactors that likely bear on human motor disorders, especially those affecting speech. Gene expression was measured in 2 basal ganglia sub-regions (area X & ventral striato-pallidum (VSP)) of 27 adult male zebra finches that sang different amounts of song over a 2hr period in the morning. 18 birds were allowed to sing freely, 9 birds were discouraged from singing by the presence of an investigator and those that sang fewer than 10 song motifs were considered “non-singers”.

2012-01-04 | E-GEOD-34819 | biostudies-arrayexpress

Core and region enriched networks of behaviorally regulated genes: the singing epigenome

Project description:We queried a songbird brain to discover behaviorally regulated transcriptional mechanisms relevant for speech behavior. About 10% of zebra finch genes showed regulation during singing, and most were brain-region specific. We propose that the brain-regional diversity of the singing-regulated gene networks is derived both from differential combinatorial binding of transcription factors and the epigenetic state of these genes before singing begins. To test this hypothesis, we measured H3K27ac two brain regions that participate in song production.

2014-12-08 | GSE63936 | GEO

Core and region enriched networks of behaviorally regulated genes: the singing epigenome

2014-12-08 | E-GEOD-63936 | biostudies-arrayexpress

Singing female songbirds: Female-specific gene networks in the song area HVC

Project description:In this data set, we compared the expression data of song nuclei HVC, visual cortex entopallium, and the molecular layer of the cerebellum dissected from females and males of 3 songbird species (S. canaria, U. cyanocephalus, P. bicolor) to identify sex-specific stimulated gene expression. Testosterone-treated male and female canaries were also included in order to study whether testosterone effect on transcriptomes is sex-specific. Finally, testosterone-treated female canaries were compared with a rare group of spontaneously singing female canaries to study whether testosterone stimulation would be different from natural stimulation.

2019-03-31 | GSE83674 | GEO

The genome of the zebra finch, a songbird

Project description:This study was part of a larger study on the zebra finch genome (Warren et al 2010. Nature). Here we present a summary of the specific experiment on singing-regulated gene expression. To evaluate the genomic landscape of learned vocal communication, we profiled gene expression in the zebra finch song nucleus, Area X, with custom Agilent oligoarrays for up to seven hours following initiation of singing. We developed algorithms to identify singing-regulated transcripts related to time spent singing, and discovered over 800 transcripts in Area X that are significantly regulated by singing. These included known increases of the egr1 and c-fos transcription factors, and a decrease in the FoxP2 transcription factor, a gene associated with spoken language development. We clusted the singing-regulated genes in Area X into 20 temporal dynamic expression patterns, which include rapidly up-regulated and transient, rapidly up-regulated and sustained, slowly up-regulated and sustained, a late upregulated response, and equally diverse clusters of down-regulated patterns. Using promotor motif search algorithms, we found significant over-representation of transcription factor binding sites in the promoters of genes within specific clusters. These binding sites included those of transcription factors known to be activated by neural activity and plasticity, such as CREB, SRF, AP-1, NFKB1, CFOS, EGR1, and MEF2. Gene expression in Area X was measured before singing (0) or after singing for 0.5, 1, 2, 3, 4, 5, 6, and 7hours. Six independent experiments were performed at each of the 9 timepoints.

2010-05-15 | E-GEOD-19900 | biostudies-arrayexpress

The genome of a songbird

2010-01-16 | GSE19900 | GEO

Singing female songbirds: Female-specific gene networks in the song area HVC

Project description:Singing female songbirds: Female-specific gene networks in the song area HVC

| PRJNA326680 | ENA

Weighted gene co-expression network analysis on microarray data from subregions of zebra finch (Taeniopygia guttata) basal ganglia

2012-01-04 | GSE34819 | GEO

De novo assembly and annotation of the singing mouse genome

Project description:De novo assembly and annotation of the singing mouse genome

| PRJNA878522 | ENA