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84 results for “reference genes”
Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication<br>The data contains two files, namely genome file and genome annotation file:<br>1. Genome:<br>This file contains 12 genomes for 5 species (cultivar), namely: <em>Malus domestica</em> cv. ‘Golden Delicious’ (GD), <em>Malus domestica</em> cv. ‘Gala’ (Gala), <em>Malus domestica</em> cv. ‘Honeycrisp’ (HC), <em>Malus domestica</em> cv. ‘HFTH1’ (HFTH1), <em>Malus baccata</em> (Mba), <em>Malus sieversii</em> (Msi), and <em>Malus sylvestris</em> (Msy)</p> <p>2. Genome annotation:<br>Corresponding to the genome file.<br>Note: Hap1 and hap2 represent two haplotypes of a species (cultivar), all data used for the construction of pan-genomes and comparative genomics analysis.</p>
Fig. 4 The probability density P in Range of a Palearctic uraniid moth Eversmannia exornata (Lepidoptera: Uraniidae: Epipleminae) was split in the Holocene, as evaluated using histone H1 and COI genes with reference to the Beringian disjunction in the genus Oreta (Lepidoptera: Drepanidae)
Fig. 4 The probability density P of the Bayesian coalescent estimation of the time of existence of the most recent common ancestors, T, of the recent representatives of O. rosea (A) and of the three northernmost species of the genus Oreta occurring at opposite sides of the Pacific: O. rosea (North America), O. pulchripes and O. paki (East Asia) (B)
Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
<p><span>The slow-evolving invertebrate amphioxus has an irreplaceable role in advancing our understanding into vertebrate origin and innovations. Here we resolve the nearly complete chromosomal genomes of three amphioxus species, one of which best recapitulates the 17 chordate ancestor linkage groups. We reconstruct the fusions, retention, or rearrangements between descendants of whole genome duplications (WGDs), which gave rise to the extant microchromosomes that likely existed in the vertebrate ancestor. Similar to vertebrates, the amphioxus genome gradually establishes its 3D chromatin architecture at the onset of zygotic activation and forms two topologically associated domains at the <em>Hox</em> gene cluster. We find that all three amphioxus species have ZW sex chromosomes with little sequence differentiation, and their putative sex-determining regions are nonhomologous to each other. Our results illuminate the unappreciated interspecific diversity and developmental dynamics of amphioxus genomes and provide high-quality references for understanding the mechanisms of chordate functional genome evolution.</span></p>
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
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Chromosome assembly and preliminary gene and repeat annotations for Myzomela tristrami reference genome
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Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
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Data for: Three amphioxus reference genomes reveal gene and chromosome evolution of chordates
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Nucleotide diversity of functionally different groups of immune response genes in Old World camels based on newly annotated and reference-guided assemblies
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Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus
The unicellular protozoan parasite Leishmania causes the neglected tropical disease leishmaniasis, affecting 12 million people in 98 countries. In South America where the Viannia subgenus predominates, so far only L. (Viannia) braziliensis and L. (V.) panamensis have been sequenced, assembled and annotated as reference genomes. Addressing this deficit in molecular information can inform species typing, epidemiological monitoring and clinical treatment. Here, L. (V.) naiffi and L. (V.) guyanensis genomic DNA was sequenced to assemble these two genomes as draft references from short sequence reads. The methods used were tested using short sequence reads for L. braziliensis M2904 against its published reference as a comparison. This assembly and annotation pipeline identified 70 additional genes not annotated on the original M2904 reference. Phylogenetic and evolutionary comparisons of L. guyanensis and L. naiffi with ten other Viannia genomes revealed four traits common to all Viannia: aneuploidy, 22 orthologous groups of genes absent in other Leishmania subgenera, elevated TATE transposon copies, and a high NADH-dependent fumarate reductase gene copy number. Within the Viannia, there were limited structural changes in genome architecture specific to individual species: a 45 Kb amplification on chromosome 34 was present in all bar L. lainsoni, L. naiffi had a higher copy number of the virulence factor leishmanolysin, and laboratory isolate L. shawi M8408 had a possible minichromosome derived from the 3' end of chromosome 34. This combination of genome assembly, phylogenetics and comparative analysis across an extended panel of diverse Viannia has uncovered new insights into the origin and evolution of this subgenus and can help improve diagnostics for leishmaniasis surveillance.
Phased T2T reference genome and pangenome reveal expanded resistance gene analogs in apple domestication
<p>Two haplotypes of the T2T genome of Golden Delicious apple and their annotation files</p>
Fig. 1 in Range of a Palearctic uraniid moth Eversmannia exornata (Lepidoptera: Uraniidae: Epipleminae) was split in the Holocene, as evaluated using histone H1 and COI genes with reference to the Beringian disjunction in the genus Oreta (Lepidoptera: Drepanidae)
Fig. 1 The presumed range of E. exornata (Eversmann, 1837)
Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
Data from: Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
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Data from: Leishmania naiffi and Leishmania guyanensis reference genomes highlight genome structure and gene evolution in the Viannia subgenus
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Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
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Data from: The strategic reference gene: an organismal theory of inclusive fitness
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Contradictory of gene expression signatures for clinical prognostic prediction caused by update of reference genome and annotation
GEO Series GSE143486. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Gene expression profile at single cell level of bulk liver allograft tissue isolated 12 months post-transplant in patients receiving regulatory dendritic cell therapy (STUDY) and reference standard-of
GEO Series GSE218121. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Comparison of gene expression profiles for heat-shocked and non-heat shocked stationary phase samples from heat tolerant isolates R1-0006 and R1-0007 and reference strain SL476
GEO Series GSE103418. Salmonella enterica subsp. enterica serovar Heidelberg. 18 samples. Type: Expression profiling by high throughput sequencing.
Aegilops tauschii reference genome sequence Aet v5.0 including annotation of small RNAs and reannotation of protein-coding genes
GEO Series GSE169198. Aegilops tauschii. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.