Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Phylogenetic relationships of longhorn beetles inferred from genome-scale data

PROVIDER: PRJNA1104827 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28824000_1.fastq.gz	Fastqsanger.gz
	SRR28824000_2.fastq.gz	Fastqsanger.gz
	SRR28823701_1.fastq.gz	Fastqsanger.gz
	SRR28823701_2.fastq.gz	Fastqsanger.gz
	SRR28824812_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 130

Similar Datasets

Mammalia

Project description:Phylogenetic relationships of mammals inferred using ultra conserved elements

| PRJNA390442 | ENA

The Ami and Yami aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

Project description:We combined new data with previously published data (PMID: 25877615, 26811443, 29379068, 18292342, 24297229, 27302840, 24395773 and 30846778) to compare phylogenetic relationships of the Ami and Yami aborigenes of Taiwan to groups from mainland Southeast Asia, island Southeast Asia and Oceania.

2021-08-23 | GSE152194 | GEO

RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

Project description:The genus Flaveria has been extensively used as a model to study the evolution of C4 photosynthesis as it contains both C3 and C4 species as well as a number of species that exhibit intermediate types of photosynthesis. The current phylogenetic tree of the Flaveria genus contains 21 of the 23 known Flaveria species and has been constructed using a combination of morphologicial data and three non-coding DNA sequences (nuclear encoded ETS, ITS and chloroplast encoded trnl-F). However, recent studies have suggested that phylogenetic trees inferred using a small number of molecular sequences may often be incorrect. Moreover, studies in other genera have often shown substantial differences between trees inferred using morphological data and those using molecular sequence. To provide new insight into the phylogeny of the genus Flaveria we utilize RNA-Seq data to construct a multi-gene concatenated phylogenetic tree of 17 Flaveria species. Furthermore, we use this new data to identify 14 C4 specific non-synonymous mutation sites, 12 of which (86%) can be independently verified by public sequence data. We propose that the data collection method provided in this study can be used as a generic method for facilitating phylogenetic tree reconstruction in the absence of reference genomes for the target species. 18 Flaveria sample including 11 species are sequenced, other three samples were also sequenced as out-group. In all, 21 samples.

2015-01-08 | E-GEOD-54339 | biostudies-arrayexpress

Yamadazyma tenuis

Project description:Xylose-fermenting yeast that is endosymbiont of longhorn beetles

| PRJNA33759 | ENA

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia

Project description:The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia - a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together these should broadly enable large-scale mammalian lineage tracing efforts.Cassiopeia and its benchmarking resources are publicly available at https://www.github.com/YosefLab/Cassiopeia.

2020-03-11 | GSE146712 | GEO

Project description:Phylogenetic relationships in Dendrosenecio

| PRJNA729901 | ENA

Zacco platypus

Project description:Phylogenetic relationships among Xenocyprididae

| PRJNA743720 | ENA

RNA-Seq Based Reconstruction of the Phylogenetic Tree of the Genus Flaveria (Asteraceae)

2015-01-08 | GSE54339 | GEO

coral metagenome

Project description:Phylogenetic position of the coral symbiont Ostreobium inferred from chloroplast genome data

| PRJNA362979 | ENA

CGH analysis of Campylobacter jejuni isolates previously analyzed by Multi-Locus Sequence Typing

Project description:In this experiment, we hava analyzed a set of 45 C. jejuni strains by CGH and MLST in order to investigate whether the strain relationships inferred from the analysis of a small number of loci (MLST) reflect whole-genome gene conservation patterns observed by CGH. Keywords: individual hybridizations, comparative genomic hybridization

2008-04-21 | GSE9919 | GEO

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