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Dataset results
67 results for “transcriptome reference”
Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.
Data from: De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover
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Data from: The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome
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Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
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Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives
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Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional "housekeeping" reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
Reference transcriptomes for three species of sacoglossan sea slug
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Data from: Reference-free transcriptome assembly in non-model animals from next generation sequencing data
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Data from: A whole-transcriptome approach to evaluating reference genes for quantitative gene expression studies: a case study in Mimulus
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Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors
GEO Series GSE81861. Homo sapiens. 1220 samples. Type: Expression profiling by high throughput sequencing.
Epigenomic, transcriptomic and proteomic characterizations of reference samples
GEO Series GSE268608. Homo sapiens. 12 samples. Type: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The transcriptomic response to a short day to long day shift in the reference legume Medicago truncatula
GEO Series GSE118893. Medicago truncatula. 18 samples. Type: Expression profiling by high throughput sequencing.
Inference of differentiation time for single cell transcriptomes using cell population reference data
GEO Series GSE85234. Mus musculus. 113 samples. Type: Expression profiling by high throughput sequencing.
A multi-omics dataset of human transcriptome and proteome stable reference
GEO Series GSE234201. Homo sapiens. 110 samples. Type: Expression profiling by high throughput sequencing.
Metabolic and transcriptomic responses of leaves from European potato reference cultivars with differential tolerance to long-term drought
GEO Series GSE77826. Solanum tuberosum. 48 samples. Type: Expression profiling by high throughput sequencing.
Bolitoglossa vallecula reference transcriptome
GEO Series GSE107213. Bolitoglossa vallecula. 4 samples. Type: Expression profiling by high throughput sequencing.
Reference Long-read Isoform-aware Transcriptomes of Activated Human CD4 T cells (PacBio Iso-Seq, matched to Illumina RNA-Seq Data)
GEO Series GSE229971. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Uncovering the Arabidopsis thaliana nectary transcriptome: nectary and reference tissues
GEO Series GSE15617. Arabidopsis thaliana. 59 samples. Type: Expression profiling by array.
Reference Transcriptomes of Activated Human CD4 T cells
GEO Series GSE229972. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Reference Short-Read Transcriptomes of Activated Human CD4 T cells (Illumina RNA-Seq, Matched to PacBio Iso-Seq Data)
GEO Series GSE229969. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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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.