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1,696 results for “DNA sequence”
Supplementary table, figures and DNA sequences of sorghum gene models SbiRTx430.01G455400 and SbiRTx.02G006600 that feature primers, gRNAs and indels created
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Cost-effective library preparation for whole genome sequencing with feather DNA
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Data from: Affordable de novo generation of fish mitogenomes using amplification-free enrichment of mitochondrial DNA and deep sequencing of long fragments
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Aligned and curated mtDNA sequences from: Ancient DNA of narrow-headed voles reveals common features of the Late Pleistocene population dynamics in cold-adapted small mammals
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The 153 readable DNA sequences of a diet research on Eurasian otter of Kinmen Island
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Targeted sequencing of T-DNA borders in OCP1xOGC transgenic lines of Camelina
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DNA sequences for: Synthetic control of actin polymerization and symmetry breaking in active protocells
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Data from: Accumulation curves of environmental DNA sequences predict coastal fish diversity in the Coral Triangle
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The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)
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DNA sequence data for two Roscoea species, R. stenophylla and R. australis (Zingiberaceae)
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Chamaeleo africanus DNA sequencing purity results and statistics
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A revised classification of Glossopetalon (Crossosomataceae) based on restriction site-associated DNA sequencing
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Aligned DNA sequence matrix for phylogenetic analyses in the article "Fifty years after: a taxonomic revision of the amphibian species from the Ecuadorian biodiversity hotspot Abra de Zamora, with description of two new Pristimantis species"
<p>The aligned matrices are in fasta format. Genes are arranged as follows:</p> <p>Subgenus Huicundomantis (Huicundomantis.fas):</p> <p>12S = 1–905</p> <p>16S = 906–1820</p> <p>RAG-1 = 1821–2463</p> <p> </p> <p>Genus Lynchius (Lynchius.fas):</p> <p>12S = 1–1028</p> <p>16S = 1029–2313</p> <p>RAG-1 = 2314–2925</p> <p> </p> <p>Pristimantis orestes group (Pristimantis_orestes.fas):</p> <p>12S = 1–964</p> <p>16S = 965–2041</p> <p>RAG-1 = 2042–2683</p>
Multiple alignment of DNA-B sequences from EACMV, EACMKV, EACMMV, EACMZV, SACMV (5 "species")
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Multiple alignment of ICMV and SLCMV DNA-B sequences
<p>All sequences available in GenBank as of 2019-06-03 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were adjusted with SeAl and AliView.</p> <p>Note added 2020-09-07: AJ575821 is listed in the file as ICMV based on its assignment in the NCBI Taxonomy database (taxa 341701 and 31600) but it is better classified as SLCMV.</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Recombination detection program (RDP4) results for EACMV-like DNA-B sequences (7 "species")
<p>A DNA-B multiple alignment (Zenodo record 3965023) was scanned with RDP4.97 (D. Martin et al. 2015). The input sequences belong to 7 “species”: CMMGV, EACMCV, EACMV, EACMKV, EACMMV, EACMZV, SACMV. Recombination breakpoints for events with statistical support from at least 5 of 7 methods were adjusted per the manual. These events were explicitly accepted, with the exception of one event which lost significance after adjustment of breakpoints. A CSV file with the results was exported and then saved a second time with Excel to normalize format (a comma in between every column).</p> <p>These results are described in a paper by Crespo-Bellido et al. (2021) https://doi.org/10.1128/JVI.00541-21</p>
Multiple sequence alignment of DNA-A sequences from ACMBFV, ACMV, CMMGV, EACMCV, EACMKV, EACMMV, EACMV, EACMZV, SACMV, ICMV, SLCMV (11 species)
<p>All full-length DNA-A sequences available in GenBank as of July 2019 were downloaded via the Taxonomy Browser interface. Sequence names were normalized/simplified and orientations of these circular sequences were standardized to begin at the replication origin nick site. Sequences were aligned with MUSCLE and alignments were manually adjusted with SeAl (A. Rambaut) and AliView (A. Larsson).</p>
Microsatellite genotypes and ITS2 DNA sequence data for Seriatopora hystrix
<p>Coral reefs provide essential goods and services but are degrading at an alarming rate due to local and global anthropogenic stressors. The main limitation that prevents the implementation of adequate conservation measures is that connectivity and genetic structure of populations are poorly known. Here, the genetic diversity and connectivity of the brooding scleractinian coral, <i>Seriatopora hystrix</i> were assessed at two scales by genotyping ten microsatellite markers for 356 individual colonies. Seriatopora hystrix showed high differentiation, both at large scale between the Red Sea and the Western Indian Ocean (WIO), and at smaller scale along the coast of East Africa.As such high levels of differentiation might indicate the presence of more than one species, a haploweb analysis was conducted with the nuclear marker ITS2, confirming that the Red Sea populations are genetically distinct from the WIO ones.Based on microsatellite analyses three groups could be distinguished within the WIO: (I) north Madagascar, (II) south-west Madagascar together with one site in northern Mozambique (Nacala), and (III) all other sites in northern Mozambique, Tanzania and Kenya. These patterns of restricted connectivity could be explained by the short pelagic larval duration of <i>S. hystrix,</i> and/or by oceanographic factors, such as eddies in the Mozambique Channel (causing larval retention in northern Madagascar but facilitating dispersal from northern Mozambique towards south-west Madagascar). This study provides an additional line of evidence supporting the conservation priority status of the Northern Mozambique Channel and should inform coral reef management decisions in the region.</p> <p> </p>
Transcriptome analysis of WT versus H2A.J-KO MEFs for the paper entitled: The H2A.J histone variant contributes to Interferon-Stimulated Gene expression in senescence by its weak interaction with H1 and the derepression of repeated DNA sequences
<p>Abstract for overall study:</p> <p>The histone variant H2A.J was previously shown to accumulate in senescent human fibroblasts with persistent DNA damage to promote inflammatory gene expression, but its mechanism of action was unknown. We show that H2A.J accumulation contributes to weakening the association of histone H1 to chromatin and increasing its turnover. Decreased H1 in senescence is correlated with increased expression of some repeated DNA sequences, increased expression of STAT/IRF transcription factors, and transcriptional activation of Interferon-Stimulated Genes (ISGs). The H2A.J-specific Val-11 moderates the transcriptional activity of H2A.J, and H2A.J-specific Ser-123 can be phosphorylated in response to DNA damage with potentiation of its transcriptional activity by the phospho-mimetic S123E mutation. Our work demonstrates the functional importance of H2A.J-specific residues and potential mechanisms for its function in promoting inflammatory gene expression in senescence.</p> <p>Specific description for this dataset:</p> <p>We further tested a role for H2A.J in Interferon-Stimulated Gene expression by analyzing the transcriptome of WT and H2A.J MEFs induced into senescence by etoposide. TruSeq stranded DNA libraries were prepared from polyA-selected RNA and sequenced as 43 bp paired-end reads. The fastq sequences were mapped to Gencode.vM24.transcripts.fa.gz (GRCm38 transcriptome) with salmon. Read counts were then aggregated to the gene level with tximeta, and differential gene expression was analysed with DESeq2, edgeR, and limma-voom. Gene set enrichment analysis was performed with camera.</p> <p>The transciptomes of senescent WT and H2AFJ-KO showed strong separation from proliferating MEFs, and a weaker separation distinguished WT and H2A.J-KO MEFs. Strikingly, gene set enrichment analysis indicated highly significant defects in Interferon Response Gene Expression in the H2A.J-KO MEFs in senescence with significant down-regulation in senescent H2A.J-KO cells of a series of oligoadenylate synthase genes (Oas1g, Oas1a, Oasl1, Oas2, Oasl2) and several ISGs. Thus, H2A.J also contributes to ISG expression in the heterologous context of senescent MEFs.</p>
SNP discovery in Cryptomeria japonica var. sinensis using restriction-site associated DNA sequencing (RAD-seq)
<p>Our study is the first to explore the genetic composition of ancient <i>Cryptomeria</i> trees across distribution range in China. <i>Background and Objectives:</i> <i>Cryptomeria japonica </i>var. <i>sinensis</i> is a native forest species of China; it is widely planted in the south of the country to create forests and for wood production. Unlike <i>Cryptomeria</i> in Japan, genetic Chinese<i> Cryptomeria </i>has seldom been studied, although there is ample evidence of its great ecological and economic value. <i>Materials and Methods:</i> Because of overcutting, natural populations are rare in the wild. In this study, we investigated seven ancient tree populations to explore the genetic composition of Chinese <i>Cryptomeria</i> through ddRAD-seq technology. <i>Results:</i> The results reveal lower genetic variation but higher genetic differentiation (<i>Ho</i>=0.143, <i>F<sub>ST</sub></i>=0.1204) than Japanese <i>Cryptomeria </i>(<i>Ho</i>=0.245, <i>F<sub>ST</sub></i>=0.0455). The 86% within-population variation is based on analysis of molecular variance (AMOVA). Significant excess heterozygosity was detected in three populations and some outlier loci were found; these were considered to be the consequence of selection or chance. STRUCTURE analysis and dendrogram construction divided the seven ancient tree populations into four groups corresponding to the geographical provinces in which the populations are located, but there was no obvious correlation between genetic distance and geographic distance. Demographic history analysis conducted by a Stairway Plot showed that the effective population size of Chinese <i>Cryptomeria</i> had experienced a continuing decline from the mid-Pleistocene to the present. Our findings suggest that strong genetic drift caused by climate fluctuation and intense anthropogenic disturbance together contributed to the current low diversity and structure. Considering the species' unfavorable conservation status, strategies are urgently required to preserve the remaining genetic resources.</p>
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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.
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.