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Dataset results
78 results for “reference sequence”
Revealing novel transcribed sequences absent from the human reference genome by RNA-Seq
GEO Series GSE30251. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods
GEO Series GSE75823. Homo sapiens. 11 samples. Type: Expression profiling by high throughput sequencing.
Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry
<p>(P0652) Genotyping-By-Sequencing and Reference Genome Enabled Variant Discovery in Octoploid Strawberry</p> <p>Genotyping-by-sequencing (GBS) approaches have enabled routine high-density genome-wide DNA variant discovery in numerous agriculturally important species. Applications of GBS in octoploid (2n = 8x = 56) strawberry (Fragaria × ananassa) have been hindered by the absence of a reference genome for physically mapping DNA sequences; for discovering variants with sub-genome resolution, or effectively distinguishing homologous from homeologous variation. High-quality reference genome assemblies have recently emerged, supplying the foundation for this study, which focused on demonstrating the utility of GBS for calling sub-genome specific DNA variants in octoploid strawberry. To reduce genomic DNA complexity, double-digest protocols were tested on diverse accessions with two restriction enzyme combinations (PstI-MseI and HindIII-MseI). GBS libraries were sequenced on an Illumina HiSeq 4000 using a 150 bp paired-end protocol. For the purpose of this study, we describe the deployment of a flexible bioinformatic pipeline for GBS-facilitated variant discovery in octoploid strawberry. The percentage of uniquely mapped reads ranged from 51.41% for PstI-MseI to 55.56% for HindIII- MseI resulting in 1,591,764 and 2,362,556 unique locations, respectively. The number of discovered variants was 2.5-fold greater for HindIII-MseI (491,811) than PstI-MseI (199,486). The GBS protocols uncovered a dense genome-wide landscape of DNA variants for high- precision genetic mapping, identification of DNA variants associated with agriculturally important phenotypes, genomic-enabled breeding, and other applications in octoploid strawberry.</p> <p>Poster: PDF of poster and abstract for PAG 2018 (P0652)</p> <p>Figures: PNGs of figures on the poster</p> <p>Scrips: Txt files of SLURM scripts used to generate the follow .vcf files.</p> <p>- 8x_GBS_0_index: Uses BWA to index the reference genome (Edger et al 2019) for later use.</p> <p>- 8x_GBS_1_Demultiplex: Used Sabre to demultiplex fastq.gz files. Demultiplex_key_PE links individuals to their unique barcode.</p> <p>- 8x_GBS_2_Main: adapter removal, sequence alignment, and individual variant calling as a SLURM array. results in a .gvcf file for individuals.</p> <p>- 8x_GBS_3_Variant: population-level variant calling to a final .vcf file</p> <p>VCF: Two VCF files from the two enzyme experiments. H = HindIII-MseI; P = PstI-MseI</p>
Data from: Phased whole-genome genetic risk in a family quartet using a major allele reference sequence
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mRNA sequence data of individual Drosophila melanogaster male and female flies from 16 Drosophila Genetic Reference Panel lines reared in replicated environments
GEO Series GSE60314. Drosophila melanogaster. 851 samples. Type: Expression profiling by high throughput sequencing.
Identifying reference genes with stable expression from high throughput sequence data
GEO Series GSE40509. Thalassiosira pseudonana CCMP1335. 4 samples. Type: Expression profiling by high throughput sequencing.
Leucegene: AML sequencing (part 1-6, GRCh38 reference)
GEO Series GSE232129. Homo sapiens. 452 samples. Type: Expression profiling by high throughput sequencing.
Deep transcriptional sequencing analysis of human prostate adenocarcinoma and reference samples
GEO Series GSE24283. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Fig. 3 in High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)
Fig. 3. Map of sampling locations in Papua New Guinea where marine Gerromorpha specimens were collected. Insert table shows a breakdown of specimens collected by locality, and sorted by the life-history stage. Base map adapted from https://d-maps.com/carte.php?num_car=3845&lang=en.
Fig. 2 in High-Throughput Sequencing for Life-History Sorting and for Bridging Reference Sequences in Marine Gerromorpha (Insecta: Heteroptera)
Fig. 2. COI gene regions sequenced in aquatic Heteroptera in relation to the full-length COI (to scale). Numbers (red) beneath each line represent the number of COI sequences on GenBank that correspond to that region (last checked 7 May 2021), and the taxonomic diversity from family to species. Counts for the Folmer region include that of the mini-barcode sequences due to region overlap. Search string used: '((((((COI[Gene Name]) OR COX[Gene Name]) OR cytochrome oxidase subunit 1[Gene Name]) OR cytochrome c oxidase subunit 1[Gene Name]) OR cytochrome c oxidase subunit I) OR cytochrome oxidase subunit I[Gene Name]) AND Gerromorpha[Organism]′.
A Single-dose, Randomized, Two-period, Two-treatment, Two-sequence, Crossover Bioequivalence Study on a Olostar Tab Versus Two Co-administered Reference Products Olmesartan Medoxomil and Rosuvastatin
ClinicalTrials.gov study NCT02561884. IPD Sharing: Not stated. Countries: 0. Publications: 0.
CASSIA: a multi-agent large language model for reference free, interpretable, and automated cell annotation of single-cell RNA-sequencing data
GEO Series GSE307976. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches
GEO Series GSE303762. Homo sapiens. 38 samples. Type: Expression profiling by high throughput sequencing.
Sequencing of miRXplore Universal Reference (Miltenyi Biotec) RNA using mDOT-seq
GEO Series GSE166931. synthetic construct. 8 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Tara Pacific metabarcoding sequencing (16S, 18S, ITS2) reference & replication tables version 1
<p>The tables in this dataset associate metabarcoding sequencing files generated by Genoscope (i.e. fastq.gz files with informative filename structures; with sequencing file pairs associated to unique 'readset' identifiers; housed on their FTP server at www.genoscope.cns.fr/sadc/tarapacific/METABARCODING; with the 'METAB' sequence strategy identifier as part of the sequencing file name) with their associated 'sample-id_source' identifier; as detailed in the 'TARA-PACIFIC_samples-provenance' file part of the 'Tara Pacific samples provenance and environmental context' Zenodo publication (DOI: 10.5281/zenodo.4068292) part of the 'tarapacific' Zenodo community). The main purpose of these tables is to act as a reference to identify samples (i.e., with a single 'sample-id_source') for which sequencing replication exists, per primer set (i.e., more than one set of fastq.gz sequencing files were generated, pre primer set). In the case of replication, these tables classify the replication into three classes color coded as green (same DNA extraction, same PCR, same sequencing run, different sequencing lane), yellow (same DNA extraction, same PCR, different sequencing run) and red (different DNA extraction and/or different PCR). It should be noted that in the vast majority of cases a 'sample-id_source' associates to only one readset per primer set. For a full description of the dataset, please see the included README.</p>
Comprehensive Human Embryogenesis Reference Tool using Single-Cell RNA-Sequencing Data
GEO Series GSE254641. Homo sapiens. 2 samples. Type: Expression profiling by high throughput sequencing.
The non-reference sequence data and the gene annotation information of chicken linear pan-genome
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Multiple sequence alignments of Treponema pallidum complete genomes using three different references for mapping NGS reads
<p>Each file corresponds to the multiple sequence alignment of 75 complete Treponema pallidum genome sequences using the genomes of strains Nichols, SS14, and CDC-2 as references for mapping. This is supplemental data to the manuscript "Evolutionary processes in the emergence and recent spread of <em>Treponema pallidum</em>, the causative agent of syphilis" by Marta Pla-Díaz, Leonor Sánchez-Busó, Lorenzo Giacani, David Šmajs, Philipp P. Bosshard, Homayoun C. Bagheri, Verena J. Schuenemann, Kay Nieselt, Natasha Arora and Fernando González-Candelas</p>
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.