Ontology highlight
ABSTRACT:
PROVIDER: PRJDB15118 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:MIG seq analysis of Japanese deep-sea fishes
| PRJDB14326 | ENA
Project description:We performed RNA-seq and ATAC-seq on in vitro activated P14 CD8 T cells transduced with MIG (empty), MIG-E47, or MIG-ID2.
2021-04-02 | GSE142342 | GEO
Project description:We use the continuously replacing dentition of Lake Malawi cichlid fishes to understand de-novo tooth replacement in adult vertebrates. In this system, each tooth is replaced in a one-for-one fashion every ~50 days. Here, we explore the source of epithelial stem cells for tooth replacement.
2019-09-23 | GSE122501 | GEO
Project description:Myanmar locates in the crossroads of South Asia, Southeast Asia, and East Asia, and is known for high culture diversity in different ethnic groups. It is considered to be important for understanding human evolutionary history and genetic diversity in East Eurasia. However, relatively few studies have examined the population structure and demographic history in Myanmar to date. In this study, we analyzed more than 220,000 genome-wide SNPs in 175 new samples of five ethnic groups from Myanmar and compared them with the published data. Our results showed that the Myanmar population is intricately substructured, with the main observed clusters corresponding roughly to western/northern highlanders (Chin, Naga, and Jingpo) and central/southern lowlanders (Bamar and Rakhine). The gene flow inferred from South Asia has a substantial influence (~11%) on the gene pool of central/southern lowlanders rather than western/northern highlanders. The genetic admixture is dated around 650 years ago. These findings suggest that the genome-wide variation in Myanmar was likely shaped by the linguistic, cultural, and historical changes.
2019-12-31 | GSE74100 | GEO
Project description:We performed RNA-seq and ATAC-seq on in vitro activated P14 CD8 T cells transduced with MIG (empty), MIG-E47, or MIG-ID2.
2021-04-02 | GSE142343 | GEO
Project description:Transcripts of the gill epithelium from three different stocks of Atlantic salmon (Salmo salar) migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt) using the 16K GRASP cDNA microarray platform.
2010-06-01 | E-MEXP-2210 | biostudies-arrayexpress
Project description:Our main objectives wereto investigate the molecular mechanisms involved in metal toxicity and detoxification in the field using juvenile yellow perch subjected to differents levels of this metal exposure. Recent local adaptation to pollution has been evidenced in several organisms inhabiting environments heavily contaminated by metals. Nevertheless, the molecular mechanisms underlying adaptation to high metal concentrations are poorly understood, especially in fishes. Yellow perch (Perca flavescens) populations from lakes in the mining area of Rouyn-Noranda (QC, Canada) have been faced with metal contamination for about 90 years. Here, we examine gene transcription patterns of fish reciprocally transplanted between a reference and a metal-contaminated lake and also fish caged in their native lake. After four weeks, 111 genes were differentially transcribed in metal-naïve fish transferred to the metal-contaminated lake, revealing a plastic response to metal exposure. Genes involved in the citric cycle and beta-oxidation pathways were under-transcribed, suggesting a potential strategy to mitigate the effects of metal stress by reducing energy turnover. However, metal-contaminated fish transplanted to the reference lake did not show any transcriptomic response, indicating a reduced plastic response capability to sudden reduction in metal concentrations. Moreover, the transcription of other genes, especially ones involved in energy metabolism, was affected by caging. Overall, our results highlight environmental stress response mechanisms in yellow perch at the transcriptomic level and support a rapid adaptive response to metal exposure through genetic assimilation. Comparison between fish Op and OpâOp using a pairwise design corresponding to the cage experiment in the reference lake Opasatica (Op), comparison between fish Du and DuâDu using a pairwise design corresponding to the cage experiment in the metal contaminated lake Dufault (Du), comparison between fish from reference lake transplanted to the metal contaminated lake (OpâDu) and fish from reference lake caged in their own lake (OpâOp) using pairwise design corresponding to the experiment of metal contamination, comparison between fish from metal contaminated lake transplanted to the reference lake (DuâOp) and fish from the metal contaminated lake caged in their own lake (DuâDu) using pairwise design corresponding to the depuration experiment.
2016-01-11 | E-GEOD-76723 | biostudies-arrayexpress
Project description:East African cichlid fishes have diversified in an explosive fashion, but the (epi)genetic basis of the phenotypic diversity of these fishes remains largely unknown. Although transposable elements (TEs) have been associated with phenotypic variation in cichlids, little is known about their transcriptional activity and epigenetic silencing. Here, we describe dynamic patterns of TE expression in African cichlid gonads and during early development. Orthology inference revealed an expansion of piwil1 genes in Lake Malawi cichlids, likely driven by PiggyBac TEs. The expanded piwil1 copies have signatures of positive selection and retain amino acid residues essential for catalytic activity. Furthermore, the gonads of African cichlids express a Piwi-interacting RNA (piRNA) pathway that target TEs. We define the genomic sites of piRNA production in African cichlids and find divergence in closely related species, in line with fast evolution of piRNA-producing loci. Our findings suggest dynamic co-evolution of TEs and host silencing pathways in the African cichlid radiations. We propose that this co-evolution has contributed to cichlid genomic diversity.
2024-04-01 | GSE252804 | GEO