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1,293
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Dataset results
1,293 results for “gene sequencing”
Using RNA sequencing for identifying gene imprinting and random monoallelic expression in human placenta (SNP genotyping)
GEO Series GSE56685. Homo sapiens. 30 samples. Type: SNP genotyping by SNP array; Genome variation profiling by SNP array.
Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in Neurodevelopmental Disorders
GEO Series GSE87568. Homo sapiens. 20 samples. Type: Expression profiling by array.
Variations in the expression pattern and sequence similarity of the key genes involved in the metabolism of taxoids among three Taxus species
GEO Series GSE121523. Taxus x media; Taxus mairei; Taxus cuspidata. 9 samples. Type: Expression profiling by high throughput sequencing.
Differentially Expressed Genes for Atrial Fibrillation Identified using RNA Sequencing from Paired Human Left and Right Atrial Appendages.
GEO Series GSE128188. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
Symbiotic Transcriptome profiling of candidate genes in model legume Arachis hypogaea using Next Generation Sequencing Technology (NGS)
GEO Series GSE98997. Arachis hypogaea. 18 samples. Type: Expression profiling by high throughput sequencing.
Next Generation Sequencing Quantitative Analysis of altered expression of genes in lncRNA ELNAT1 knockdown bladder cancer cells
GEO Series GSE156461. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Nuclear RNAi Contributes to the Silencing of Off-target Genes and Repetitive Sequences in Caenorhabditis elegans
GEO Series GSE92307. Caenorhabditis elegans. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Gene expression by high-throughput sequencing of T47D-MTVL human breast cancer cells upon H1.2 knock-down
GEO Series GSE190158. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Differentially expressed genes by DMSO in mouse 2-cell embryos identified by RNA sequencing
GEO Series GSE124598. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
Sequence alignments and tree file for wsp gene.
<p>Alignment of <em>wsp</em> dataset was constructed on the GUIDANCE2 Server based on codons using the MAFFT algorithm, and ambiguous alignments with the confidence score below 0.7 were excluded. The maximum likelihood tree was built using <em>RAxML</em> program.</p>
Data from: 346 target gene sequences from Vitaceae for Hyb-Seq
<p>The Vitaceae (the grape family) consists of 16 genera and ca. 950 species. It is best known for the economically important fruit crop -- the grape <i>Vitis vinifera</i>. The deep phylogenetic relationships and character evolution of the grape family have attracted the attention of researchers in recent years. We herein reconstruct the phylogenomic relationships within Vitaceae using nuclear and plastid genes based on the Hyb-Seq approach and test the newly proposed classification system of the family. The five tribes of the grape family, including Ampelopsideae, Cayratieae, Cisseae, Parthenocisseae, and Viteae, are each robustly supported by both nuclear and chloroplast genomic data. The cupular floral disc (raised above and free from ovary at the upper part) is an ancestral state of Vitaceae, with the inconspicuous floral disc as derived in the tribe Parthenocisseae, and the state of adnate to the ovary as derived in the tribe Viteae. The 5-merous floral pattern was inferred to be the ancestral in Vitaceae, with the 4-merous flowers evolved at least two times in the family. The compound dichasial cyme (cymose with two secondary axes) is ancestral in Vitaceae and the thyrse inflorescence (a combination of racemose and cymose branching) in tribe Viteae is derived. The ribbon-like trichome only evolved once in Vitaceae, as a synapomorphy for the tribe Viteae.</p>
Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Background: The adaptive immune system generates a remarkable range of antigen-specific T-cell receptors (TCRs), allowing the recognition of a diverse set of antigens. Most of this diversity is encoded in the complementarity determining region 3 (CDR3) of the β chain of the αβ TCR, which is generated by somatic recombination of noncontiguous variable (V), diversity (D), and joining (J) gene segments. Deletion and non-templated insertion of nucleotides at the D-J and V-DJ junctions further increases diversity. Many of these gene segments are annotated as non-functional owing to defects in their primary sequence, the absence of motifs necessary for rearrangement, or chromosomal locations outside the TCR locus. Methods: We sought to utilize a novel method, based on high-throughput sequencing of rearranged TCR genes in a large cohort of individuals, to evaluate the use of functional and non-functional alleles. We amplified and sequenced genomic DNA from the peripheral blood of 587 healthy volunteers using a multiplexed polymerase chain reaction assay that targets the variable region of the rearranged TCRβ locus, and we determined the presence and the proportion of productive rearrangements for each TCRβ V gene segment in each individual. We then used this information to annotate the functional status of TCRβ V gene segments in this cohort. Results: For most TCRβ V gene segments, our method agrees with previously reported functional annotations. However, we identified novel non-functional alleles for several gene segments, some of which were used exclusively in our cohort to the detriment of reported functional alleles. We also saw that some gene segments reported to have both functional and non-functional alleles consistently behaved in our cohort as either functional or non-functional, suggesting that some reported alleles were not present in the population studied. Conclusions: In this proof-of-principle study, we used high-throughput sequencing of the TCRβ locus of a large cohort of healthy volunteers to evaluate the use of functional and non-functional alleles of individual TCRβ V gene segments. With some modifications, our method has the potential to be extended to gene segments in the α, γ, and δ TCR loci, as well as the genes encoding for B-cell receptor chains.
16S rRNA gene and ITS2 region amplicon sequencing of GBP5 KO mice and WT littermates
<p>16S rRNA gene (v4) and ITS2 region amplicon sequencing of fecal microbiota of GBP5 KO mice and their littermate WT mice.</p>
Standard sequences of six groups of ampC β-lactamase genes
<p>Standard sequences of six groups of <em>ampC</em> β-lactamase genes, ACC, EBC, CIT, DHA, MOX and FOX, were selected from GenBank to synthesize genes and confirmed by sequencing.</p>
Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation - Supplementary Data
<p>Genotype data for 19 cell lines from the Yoruba HapMap population that were used in this study, and summary statistics from QTL calling (see README.md in summary.zip).</p>
Data from: High-throughput sequencing of the T-cell receptor beta chain gene distinguishes two subgroups of cutaneous T-cell lymphoma
[No abstract entered]
Figure 1 from: Grzywacz B, Tatsuta H (2017) Phylogenetic relationship of Japanese Podismini species (Orthoptera: Acrididae: Melanoplinae) inferred from a partial sequence of cytochrome c oxidase subunit I gene. Journal of Orthoptera Research 26: 11-19. https://doi.org/10.3897/jor.26.14547
Figure 1 - A map of Japan with the distribution of nine genera of Japanese Podismini.
Figure 1 from: Grzywacz B, Tatsuta H (2017) Phylogenetic relationship of Japanese Podismini species (Orthoptera: Acrididae: Melanoplinae) inferred from a partial sequence of cytochrome c oxidase subunit I gene. Journal of Orthoptera Research 26: 11-19. https://doi.org/10.3897/jor.26.14547
Figure 1 - A map of Japan with the distribution of nine genera of Japanese Podismini.
Fig. 1 in Molecular phylogeny of Indonesian Lymantria Tussock Moths (Lepidoptera: Erebidae) based on CO I gene sequences
Fig. 1. Scatter plots of K2P model distances for transition (Ts) versus Transversion (Tv).
Supplemental Material for "Overcoming challenges in variant calling: exploring sequence diversity in candidate genes for plant development in perennial ryegrass (Lolium perenne)"
<p>Supplemental materials to the manuscript.</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.