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63 results for “massively parallel 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.
Search for New Genetic Causes of Hypercalcemia by Massively Parallel Sequencing of a Genes Panel
ClinicalTrials.gov study NCT02908542. IPD Sharing: YES. Countries: 1. Publications: 0.
Multicentric Prospective Study to Screen Inborn Errors of Metabolism in Non-immune Hydrops (NIH) Fetalis by Massively Parallel Sequencing
ClinicalTrials.gov study NCT04308603. IPD Sharing: NO. Countries: 1. Publications: 0.
The Study of Massively Parallel Sequencing in Early Detection for Gynecologic Malignant Tumor
ClinicalTrials.gov study NCT02166515. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Feasibility Study of a Molecular Karyotype Using a Very High-throughput Sequencing Approach, the "Massive Parallel Sequencing" on Circulating Tumor DNA
ClinicalTrials.gov study NCT04104633. IPD Sharing: NO. Countries: 1. Publications: 0.
ALDH2, CCNE1 and SMAD3 are Potential Prognostic Markers for Upper Tract Urothelial Carcinoma Revealed by Massively Parallel Sequencing.
GEO Series GSE47702. Homo sapiens. 20 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.
TCR sequencing paired with massively parallel 3′ RNA-seq reveals clonotypic T cell signatures
GEO Series GSE136028. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
Multiplexing and massive parallel sequencing of targeted DNA methylation to predict chronological age
GEO Series GSE267985. Homo sapiens. 390 samples. Type: Methylation profiling by high throughput sequencing.
The Complete Genome of a Single Individual by Massively Parallel DNA Sequencing
GEO Series GSE10668. Homo sapiens. 6 samples. Type: Genome variation profiling by genome tiling array; Genome variation profiling by SNP array; SNP genotyping by SNP array.
Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing
GEO Series GSE26826. Homo sapiens. 8 samples. Type: Methylation profiling by high throughput sequencing.
BART-Seq: cost-effective massively parallelized targeted sequencing for genomics, transcriptomics, and single-cell analysis
GEO Series GSE107723. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Other.
Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing
GEO Series GSE32493. Homo sapiens. 6 samples. Type: Non-coding RNA profiling by high throughput sequencing.
High-resolution mapping of copy-number alterations with massively parallel sequencing
GEO Series GSE13372. Homo sapiens. 68 samples. Type: Genome variation profiling by SNP array.
Fine-scale mapping of copy-number alterations with massively parallel sequencing
GEO Series GSE12019. Homo sapiens. 225 samples. Type: Genome variation profiling by SNP array.
Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma
GEO Series GSE63420. Homo sapiens. 30 samples. Type: Genome variation profiling by high throughput sequencing; Expression profiling by high throughput sequencing.
Use Massive Parallel Sequencing and Exome Capture Technology to Sequence the Exome of Fanconi Anemia Children and Their Patents
ClinicalTrials.gov study NCT01995305. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Massively Parallel Sequencing to Identify Microbiological Organisms in Bronchoalveolar Lavage Fluid
ClinicalTrials.gov study NCT03995030. IPD Sharing: YES. Countries: 0. Publications: 0.
Mapping of copy-number alterations with massively parallel sequencing
GEO Series GSE13373. Homo sapiens. 293 samples. Type: Genome variation profiling by SNP array.
Massively parallel saturation genome editing of an essential mitochondrial targeting sequence (TileSeq)
GEO Series GSE232150. Homo sapiens. 36 samples. Type: Other.
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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.