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3,584 results for “genomic analysis”
Whole human genome expression analysis on left ventricular free wall heart tissue samples
GEO Series GSE84796. Homo sapiens. 17 samples. Type: Expression profiling by array.
Figure 1 from: Wu Y-A, Gao J-W, Cheng X-F, Xie M, Yuan X-P, Liu D, Song R (2020) Characterization and comparative analysis of the complete mitochondrial genome of Azygia hwangtsiyui Tsin, 1933 (Digenea), the first for a member of the family Azygiidae. ZooKeys 945: 1-16. https://doi.org/10.3897/zookeys.945.49681
Figure 1 An annular diagram of the Azygia hwangtsiyui mitochondrial genome.
Figure 3 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure 3 Evolutionary rates of the Lepus yarkandensis mitogenome by Ka/Ks.
Figure 2 from: Shan W, Tursun M, Zhou S, Zhang Y, Dai H (2021) Complete mitochondrial genome sequence of Lepus yarkandensis Günther, 1875 (Lagomorpha, Leporidae): characterization and phylogenetic analysis. ZooKeys 1012: 135-150. https://doi.org/10.3897/zookeys.1012.59035
Figure 2 GC and AT skews for mitochondrial PCGs in Lepus yarkandensis.
Data from: Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in sea lamprey and Japanese lamprey
Background: Lampreys are extant representatives of the jawless vertebrate lineage that diverged from jawed vertebrates around 500 million years ago. Lamprey genomes contain information crucial for understanding the evolution of gene families in vertebrates. The ATP-binding cassette (ABC) gene family is found from prokaryotes to eukaryotes. The recent availability of two lamprey draft genomes from sea lamprey Petromyzon marinus and Japanese lamprey Lethenteron japonicum presents an opportunity to infer early evolutionary events of ABC genes in vertebrates. Results: We conducted a genome-wide survey of the ABC gene family in two lamprey draft genomes. A total of 37 ABC transporters were identified and classified into seven subfamilies; namely seven ABCA genes, 10 ABCB genes, 10 ABCC genes, three ABCD genes, one ABCE gene, three ABCF genes, and three ABCG genes. The ABCA subfamily has expanded from three genes in sea squirts, seven and nine in lampreys and zebrafish, to 13 and 16 in human and mouse. Conversely, the multiple copies of ABCB1-, ABCG1-, and ABCG2-like genes found in sea squirts have contracted in the other species examined. ABCB2 and ABCB3 seem to be new additions in gnathostomes (not in sea squirts or lampreys), which coincides with the emergence of the gnathostome-specific adaptive immune system. All the genes in the ABCD, ABCE and ABCF subfamilies were conserved and had undergone limited duplication and loss events. In the sea lamprey transcriptomes, the ABCE and ABCF gene subfamilies were ubiquitously and highly expressed in all tissues while the members in other gene subfamilies were differentially expressed. Conclusions: Thirteen more lamprey ABC transporter genes were identified in this study compared with a previous study. By concatenating the same gene sequences from the two lampreys, more full length sequences were obtained, which significantly improved both the assignment of gene names and the phylogenetic trees compared with a previous analysis using partial sequences. The ABC gene subfamilies in chordates have undergone obvious expansion or contraction. The ABCA subfamily showed the highest gene expansion rate during chordate evolution. The evolution of ABC transporters in lampreys requires further evaluation because the present results are based on a draft genome.
Data from: Genome-wide meta-analysis of sciatica in Finnish population
Sciatica or the sciatic syndrome is a common and often disabling low back disorder in the working-age population. It has a relatively high heritability but poorly understood molecular mechanisms. The Finnish population is a genetic isolate where small founder population and bottleneck events have led to enrichment of certain rare and low frequency variants. We performed here the first genome-wide association (GWAS) and meta-analysis of sciatica. The meta-analysis was conducted across two GWAS covering 291 Finnish sciatica cases and 3671 controls genotyped and imputed at 7.7 million autosomal variants. The most promising loci (p<1x10-6) were replicated in 776 Finnish sciatica patients and 18,489 controls. We identified five intragenic variants, with relatively low frequencies, at two novel loci associated with sciatica at genome-wide significance. These included chr9:14344410:I (rs71321981) at 9p22.3 (NFIB gene; p=1.30x10-8, MAF=0.08) and four variants at 15q21.2: rs145901849, rs80035109, rs190200374 and rs117458827 (MYO5A; p=1.34x10-8, MAF=0.06; p=2.32x10-8, MAF=0.07; p=3.85x10-8, MAF=0.06; p=4.78x10-8, MAF=0.07, respectively). The most significant association in the meta-analysis, a single base insertion rs71321981 within the regulatory region of the transcription factor NFIB, replicated in an independent Finnish population sample (p=0.04). Despite identifying 15q21.2 as a promising locus, we were not able to replicate it. It was differentiated; the lead variants within 15q21.2 were more frequent in Finland (6-7%) than in other European populations (1-2%). Imputation accuracies of the three significantly associated variants (chr9:14344410:I, rs190200374, and rs80035109) were validated by genotyping. In summary, our results suggest a novel locus, 9p22.3 (NFIB), which may be involved in susceptibility to sciatica. In addition, another locus, 15q21.2, emerged as a promising one, but failed to replicate.
Figure 3 from: Li W, Qiu N, Du H (2022) Complete mitochondrial genome of Rhodeus cyanorostris (Teleostei, Cyprinidae): characterization and phylogenetic analysis. ZooKeys 1081: 111-125. https://doi.org/10.3897/zookeys.1081.77043
Figure 3 Putative secondary structures of the 22 tRNAs of Rhodeus cyanorostris.
Figure 3 in Taxonomic changes suggested by the genomic analysis of Hesperiidae (Lepidoptera)
Figure 3. Genomic tree of Tagiadinae. See Fig. 1 legend for notations.
Data from: A multi-breed genome-wide association analysis for canine hypothyroidism identifies a shared major risk locus on CFA12
[No abstract entered]
De novo assembly of the polyhydroxybutyrate (PHB) producer Azohydromonas lata strain H1 (Pelleroni and Pelleroni, 1978) genome and genomic analysis of PHB production machinery
Open the record for dataset details and reuse information.
Figure 3 from: Zhang Q-H, Huang P, Chen B, Li T-J (2018) The complete mitochondrial genome of Orancistrocerus aterrimus aterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae). ZooKeys 790: 127-144. https://doi.org/10.3897/zookeys.790.25356
Figure 3 Nucleotide composition of all 13 PCGs of eleven species of Vespidae.
Figure 1 from: Yang M, Hu B, Zhou L, Liu X, Shi Y, Song L, Wei Y, Cao J (2019) First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera. ZooKeys 879: 137-156. https://doi.org/10.3897/zookeys.879.35101
Figure 1 Mitochondrial genome map of the Yponomeuta montanatus.
Data from: Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon
In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.
Comparative genomics analysis of the aromatic and xenobiotic degradation capacities and heavy metal resistance in seven environmentally-derived bacterial isolates.
<p>Annotations and datasets generated from the comparative genomics analyses.</p>
ROAR-DIGAP: A Widely Inclusive, Largely Virtual Pilot Trial Utilizing DIGAP (Deep Integrated Genomics Analysis Platform) To Personalize Treatments
ClinicalTrials.gov study NCT06429059. IPD Sharing: NO. Countries: 1. Publications: 0.
Genome-wide Analysis of Single Nucleotide Polymorphisms of Brain Arteriovenous Malformations and Cerebral Aneurysm
ClinicalTrials.gov study NCT01801488. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Tissue Acquisition and Genomics Analysis of Breast Cancer and Other Gynecologic Malignancies
ClinicalTrials.gov study NCT03762733. IPD Sharing: YES. Countries: 1. Publications: 0.
Cancer Genome Analysis
ClinicalTrials.gov study NCT01458704. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Analysis of Human Genomic DNA in Embryo's Culture Media
ClinicalTrials.gov study NCT02359747. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Correlative Analysis of the Genomics of Vitamin D and Omega-3 Fatty Acid Intake in Prostate Cancer
ClinicalTrials.gov study NCT03290417. IPD Sharing: Not stated. Countries: 1. Publications: 0.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.