Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Estrildid_finches_gut_microbiota

ABSTRACT: The gut microbial composition is species-specific and individual-specific in two species of estrildid finches, the Bengalese finch and the zebra finch

PROVIDER: PRJEB41573 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR4894120_1.fastq.gz	Fastqsanger.gz
	ERR4894120_2.fastq.gz	Fastqsanger.gz
	ERR4894140_1.fastq.gz	Fastqsanger.gz
	ERR4894140_2.fastq.gz	Fastqsanger.gz
	ERR4894150_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 408

Similar Datasets

Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

Project description:We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.

2010-02-11 | GSE20035 | GEO

Interspecific single-cell transcriptomic analysis reveals differences in signaling pathways governing gonadal primordial germ cells between chicken and zebra finch (Taeniopygia guttata) [chicken scRNA-seq]

Project description:Primordial germ cells (PGCs), major cell resource used in the production of germline chimeras in birds, have been used in conservation of avian genetic resources and production of transgenic animals. Numerous bird species have been put on the brink of extinction due to habitat loss and degradation caused by environmental destruction and climate change, but research on PGCs is limited to specific poultry, such as chickens. Although it has recently been expanding to various bird species, it is still difficult to utilize PGCs due to biological differences and difficulties in in vitro long-term culture. Here, we constructed a single-cell landscape of chicken gonadal PGCs with established long-term culture systems of PGCs and compared them with those of the vocal learning wild bird, the zebra finches. Our results identified the interspecific differences in signaling pathways in gonadal PGCs and somatic cells, respectively. In particular, the NODAL and insulin signaling pathways were more active in zebra finch than in chickens, whereas the FGF downstream signaling pathway known to be important for the proliferation of chicken PGCs, was more active in chickens. These differences may contribute to optimizing the in vitro culture conditions of zebra finch PGCs. This study is the first cross-species single-cell transcriptomic analysis targeting birds, and laid an essential groundwork to contribute to the restoration of endangered birds and the production of transgenic birds by securing sufficient PGCs from various bird species in the future.

2023-11-28 | GSE208178 | GEO

single nuclei RNA-seq at RA in juvenile zebra finch and owl finch F1 hybrid birds

Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.

2023-11-04 | GSE217341 | GEO

single nuclei RNA-seq at Area X in juvenile zebra finch and owl finch F1 hybrid birds

Project description:To investigate the cellular basis of parental species bias at birdsong, we performed single nuclei RNA-seq for six zebra finch and owl finch F1 hybrid juvenile birds.

2023-11-04 | GSE217340 | GEO

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RRBS]

Project description:Song learning in zebra finches is a prototypical example of a complex learned behavior, yet knowledge on the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 dph and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA (hydroxy)methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age dependent gene expression was found for various transcription factors (i.a. OTX2, AR and FOS) involved in neurodevelopment. Additionally, genomic regions featured by age dependent differential methylation in differentially expressed genes were significantly enriched for specific transcription factor binding motifs. Incomplete dosage compensation was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.

2021-04-07 | GSE147973 | GEO

DNA methylation regulates transcription factor specific neurodevelopmental but not sexually dimorphic gene expression dynamics in zebra finch telencephalon [RNA-Seq]

2021-04-07 | GSE147972 | GEO

Transcription profiling of upper beak primorida of five species of Darwins Finches to identify species and/or size specific transcripts

Project description:We used five different species of Darwins Finches (G. magnirostris, G. conirostris, G. fortis, G. scandens, G. difficilis). G. difficilis was used as a common reference and we polled RNA from 9 unrelated individuals of this species to lower variation. We used at least two unrelated individual embryos from each of the more derived species. We first made cDNA library from the upper beak primordia tissue, which was used to print microarrays. Next, we collected upper beak primordia from stage 26 embryos of 5 species of Darwins Finches that differed in their beak morphology, for making Cy3- and Cy5-labeled probes with the most basal species, the Sharp-beaked Finch, serving as a reference. We then clustered the obtained expression profiles to find transcripts that were expressed in a species- and/or size-specific manner.

2022-11-21 | E-MEXP-702 | biostudies-arrayexpress

Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds

2010-02-10 | E-GEOD-20035 | biostudies-arrayexpress

Individual- and species-specific skin microbiomes in three different estrildid finch species revealed by 16S amplicon sequencing

Project description:Individual- and species-specific skin microbiomes in three different estrildid finch species revealed by 16S amplicon sequencing

| PRJEB23205 | ENA

Comparative genomic hybridization of zebra finch and common whitethroat samples using a Affymetrix custom array designed for the zebra finch

Project description:We have conducted a Cross-Species Microarray analysis by hybridizing genomic DNA from the common whitethroat (Sylivia communis) on a newly developed Affymetrix costum array designed for the zebra finch (Taeniopygia guttata), the Lund-zf array. We have also quality tested the Lund-zf array by hybridizing zebra finch genomic DNA to the platform.

2007-09-30 | E-MEXP-1181 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data