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Dataset results
89 results for “sequence annotation”
Data from: Gene prediction and annotation in Penstemon (Plantaginaceae): a workflow for marker development from extremely low-coverage genome sequencing
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Annotating Low Abundance and Transient RNAs in Yeast using Ultra High-throughput Sequencing
GEO Series GSE11801. Saccharomyces cerevisiae. 16 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.
Improved annotation of C. elegans microRNAs by deep sequencing reveals structures associated with processing by Drosha and Dicer
GEO Series GSE24704. Caenorhabditis elegans. 1 samples. Type: Non-coding RNA profiling by high throughput sequencing.
RNA sequencing of Cercospora zeina grown in vitro to annotate gene models
GEO Series GSE90705. Cercospora zeina. 7 samples. Type: Expression profiling by high throughput sequencing.
Deep sequencing, profiling and detailed annotation of miRNAs in Takifugu rubripes
GEO Series GSE65404. Takifugu rubripes. 9 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Refining mouse annotations via targeted RNA sequencing
GEO Series GSE72311. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Annotating Low Abundance and Transient RNAs in Yeast using Tiling Microarrays and Ultra High-throughput Sequencing
GEO Series GSE11802. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by high throughput sequencing; Expression profiling by genome tiling array.
High resolution annotation of Zebrafish transcriptome using long-read sequencing
GEO Series GSE101843. Danio rerio. 4 samples. Type: Expression profiling by high throughput sequencing.
Application of annotation-agnostic RNA sequencing data analysis tools for biomarker discovery in liquid biopsy.
GEO Series GSE183942. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Spatially Annotated Single Cell Sequencing for Unraveling Intratumor Heterogeneity
GEO Series GSE196245. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
CHO smallRNA sequencing for microRNA annotation
GEO Series GSE59838. Cricetulus griseus. 12 samples. Type: Non-coding RNA profiling by high throughput sequencing.
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.
MiRLog and dbmiR: prioritization and functional annotation tools to study human microRNA sequence variants
<p>dbmiR is a comprehensive database for functional annotation of miRNA SNVs (Single Nucleotide Variants). It includes a precompiled list of all possible miRNA allelic SNVs, providing their biological annotations at nucleotide and miRNA levels. In dbmiR we also integrated MiRLog, a new meta-predictor we implemented to predict the functional effect of miRNA SNVs.</p> <p>dbmiR can be used only for non-commercial purposes because of the licenses associated with some of the included tools and databases.</p>
Structural annotation of equine protein-coding genes determined by mRNA sequencing
GEO Series GSE21925. Equus caballus. 8 samples. Type: Expression profiling by high throughput sequencing.
Data from: Annotation of pseudogenic gene segments by massively parallel sequencing of rearranged lymphocyte receptor loci
Open the record for dataset details and reuse information.
High resolution and allelic-specific annotation of preimplantation embryo transcriptome using long-read sequencing
GEO Series GSE138760. Mus musculus. 21 samples. Type: Expression profiling by high throughput sequencing.
Sequence data for annotation and scaffolding of the Lathyrus sativus LS007 Rbp1.0 genome assembly
GEO Series GSE223956. Lathyrus sativus. 35 samples. Type: Expression profiling by high throughput sequencing; Other.
Deep sequencing and functional annotation reveal miRNAs implicated in the cell senescence phenotype
GEO Series GSE27404. Homo sapiens. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Bulk RNA sequencing data of rice root sections for Single-cell RNA-seq developmental stage annotation
GEO Series GSE260671. Oryza sativa. 30 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
Understand access before you commit
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.