Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genome diversification analysis

PROVIDER: PRJNA699136 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13617225_1.fastq.gz	Fastqsanger.gz
	SRR13617225_2.fastq.gz	Fastqsanger.gz
	SRR13617226_1.fastq.gz	Fastqsanger.gz
	SRR13617226_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

TR study of ‘A multi-center proof-of-concept phase2 study of encorafenib + binimetinib + cetuximab in patients with BRAF non-V600E mutated metastatic colorectal cancer (BIGBANG study)&quot

Project description:Primary outcome(s): Cancer related genome analysis, gene expression and molecular characterization analysis

| 2647002 | ecrin-mdr-crc

The Ecoresponsive Genome of Daphnia pulex: Empirical annotation of the Daphnia pulex genome

Project description:This SuperSeries is composed of the following subset Series: GSE25841: Evolutionary Diversification of Duplicated Genes; Experiment A GSE25843: Evolutionary Diversification of Duplicated Genes; Experiments B-I, M-P GSE25845: Evolutionary Diversification of Duplicated Genes; Experiments B-I GSE25850: Evolutionary Diversification of Duplicated Genes; Experiment J GSE25851: Evolutionary Diversification of Duplicated Genes; Experiment L, K GSE25852: Empirical Annotation of the Daphnia pulex genome; Experiment B GSE25855: Empirical Annotation of the Daphnia pulex genome; Experiment A GSE25856: Empirical Annotation of the Daphnia pulex genome; Experiment C Refer to individual Series

2011-02-01 | E-GEOD-25823 | biostudies-arrayexpress

Research on genomic test utilizing next generation sequencer for solid tumors and development of the genome database

Project description:Interventions: Genomic test CANCERPLEX-JP OncoGuide NCC oncopanel system FndationONe CDx genome profile GUARDANT360 MSI Analysis System BRACAnalysis Primary outcome(s): Development of genome database Study Design: Single arm Non-randomized

| 2643590 | ecrin-mdr-crc

Hagfish genome elucidates vertebrate whole genome duplication events and their evolutionary consequences

Project description:Polyploidy or whole genome duplication (WGD) is a major event that drastically reshapes genome architecture and is often assumed to be causally associated with organismal innovations and radiations. The 2R Hypothesis suggests that two WGD events (1R and 2R) occurred during early vertebrate evolution. However, the timing of the 2R event relative to the divergence of gnathostomes (jawed vertebrates) and cyclostomes (jawless hagfishes and lampreys) is unresolved and whether these WGD events underlie vertebrate phenotypic diversification remains elusive. Here we present the genome of the inshore hagfish, Eptatretus burgeri. Through comparative analysis with lamprey and gnathostome genomes, we reconstruct the early events in cyclostome genome evolution, leveraging insights into the ancestral vertebrate genome. Genome-wide synteny and phylogenetic analyses support a scenario in which 1R occurred in the vertebrate stem-lineage during the early Cambrian, and the 2R event occurred in the gnathostome stem-lineage, maximally in the late Cambrian-earliest Ordovician, after its divergence from cyclostomes. We find that the genome of stem-cyclostomes experienced at least an additional, independent genome triplication. Functional genomic and morphospace analyses demonstrate that WGD events generally contribute to developmental evolution with similar changes in the regulatory genome of both vertebrate groups. However, appreciable morphological diversification occurred only after the 2R event, questioning the general expectation that WGDs lead to leaps of bodyplan complexity.

2023-11-22 | GSE247552 | GEO

Antigen exposure reshapes chromatin architecture in central memory CD8+ T cells and imprints enhanced recall capacity [ATAC-seq]

Project description:Compared with naïve CD8+ T cells, antigen-experienced effector and central memory CD8 T cells show extensive CTCF redistribution and 3D genome reorgainzation, which underlie the transcriptomic diversification as well as recall capacity in response to secondary challenges.

2023-11-26 | GSE244999 | GEO

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Project description:Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.

2021-08-19 | GSE158514 | GEO

Evaluation of phenotypic plasticity in Rana temporaria tadpole development

Project description:Traditionally, the study of evolution has focused on heritable variation, because selection on non-heritable phenotypic variation was deemed non-important for its inability to cause evolutionary responses such as diversification of lineages. Recently however, it has been suggested that also environmentally induced phenotypic variation such as phenotypic plasticity can play an important role in adaptive responses resulting in diversification. The purpose of this study is to investigate the importance of phenotypic plasticity for the diversification of lineages, using life history, morphological traits, and genomic profiling during post embryonic development in plastic and non-plastic genotypes of the common frog Rana temporaria. Six animals each originating from four different islands were reared in either constant or reduced water conditions and hepatic mRNA levels of Gosner stage 37 animals evaluated by MAGEX DNA array analysis.

2014-03-18 | E-GEOD-42274 | biostudies-arrayexpress

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)

Project description:Venomous animals have traditionally been studied from a proteomic (but also transcriptomic) perspective, often overlooking the study of venom from a genomic point of view until recently. The rise of genomics has led to an increase in the number of reference genomes for non-model organisms, including venomous taxa, enabling new questions on venom evolution from a genomic context. Although venomous snakes are the fundamental model system in venom research, the number of high-quality reference genomes in the group remains limited. In this study, we present a high-quality chromosome-level reference genome for the Arabian horned viper (Cerastes gasperettii), a highly venomous snake native to the Arabian Peninsula. Our highly-contiguous genome allowed us to explore macrochromosomal rearrangements within the Viperidae family, as well as across squamate reptile evolution. Furthermore, we identified a total of ten different toxins conforming the venom’s core, in line with our proteomic results. We also compared microsyntenic changes in the main toxin gene clusters with those of other venomous snake species, highlighting the pivotal role of gene duplication and loss in the emergence and diversification of the two main toxin families for Cerastes gasperettii. Using Illumina data, we reconstructed the demographic history and genome-wide diversity of the species, revealing how historical aridity likely drove population expansions. Finally, this study highlights the importance of using long-read sequencing as well as chromosome-level reference genomes to disentangle the origin and diversification of toxin families in venomous species.

2025-02-18 | PXD060783 | Pride

Chromosome-level reference genome for the medically important Arabian horned viper (Cerastes gasperettii)

2025-02-18 | PXD060777 | Pride

TR accompanied with the study titled A multicenter phase II study of Nivolumab monotherapy in recurrent and/or metastatic gastrointestinal cancer patients with high Tumor Mutation Burden (TMB-H).

Project description:Primary outcome(s): 1. Evaluation of genome abnormality and gene expression by omics analysis of tumor etc. 2. TCR repertoire analysis and RNA expression analysis etc. of T cells in tumor tissue and peripheral blood. 3. Prediction and identification of tumor neo-antigen and evaluation of immunogenicity etc. 4. Analyze ctDNA(16S rRNA PCR) and feces of patients with advanced solid malignancies over time to profile and monitor cancer-related genomic alterations 5. Assessment of the relationship between the analysis above and clinical pathological features or therapeutic efficacy etc.

| 2648665 | ecrin-mdr-crc

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