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725 results for “Isoforms”
the transcriptome GTFs, FASTA and SQANTI reports for short-read assembled isoforms, long-read assembled isoforms and our assembled isoforms
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Dataset of Selectivity study of diaminopyrimidine-based inhibitors of MTHFD isoforms.
<p>Dataset of co-crystallized poses, redocking poses and docking poses, and MD simulation trajectories of diaminopyrimdine-based compounds 1-3 bound to MTHFD1, MTHFD2 and MTHFD2L isoforms. </p>
Analysis of NSD3 Isoform Expression from TCGA-LUSC Data
<p><strong>SGC Open Notebook Project to Characterize the HMTase NSD3</strong></p> <p><strong>Exp028 Objective: </strong>There are two major NSD3 isoforms expressed, long (aa 1-1437) and short (aa 1-645, differing in sequence from 620-645). Importantly, the short isoform was shown to be required for the maintenance of acute myeloid leukemia (AML) [1]. This isoform lacks a SET domain and thus methyltransferase activity. It is not clear if the two isoforms are co-expressed or independently regulated. As a first attempt to study differential regulation of the two isoforms, I have used the TCGA-LUSC dataset to analyze relative expression levels in the context of squamous cell lung cancer (LUSC) [2]. </p> <p><strong>References:</strong> </p> <p>1. Shen C, Ipsaro JJ, Shi J, et al. NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler. Molecular cell. 2015;60(6):847-859. doi:10.1016/j.molcel.2015.10.033. <br> 2. Weinstein JN, Collisson EA, Mills GB, et al. The Cancer Genome Atlas Pan-Cancer Analysis Project. Nature genetics. 2013;45(10):1113-1120. doi:10.1038/ng.2764.</p>
Test dataset for Combined Isoform Assembly pipeline
<p>This is a test dataset for Carlos Alfonso-Gonzalez's "Combined Isoform Assembly" pipeline. Refer to the project github for instructions on how to run it.</p>
Supplementary Tables for Paper "Hidden genetic regulation of human complex traits via brain isoforms"
<p>Supplementary Tables for Paper "Hidden genetic regulation of human complex traits via brain isoforms".</p>
Isoform analysis Galaxy training
<p>Datasets required for the training</p>
isoMiGA: Long-read isoforms discovered in human microglia
<p>https://github.com/RajLabMSSM/isoMiGA </p> <p>Novel isoform discovery from long-read RNA-seq of 30 human microglia samples with PacBio CCS.</p> <p><strong>Isoform sets used</strong></p> <p>isomiga_full: all isoforms discovered from hybrid assembly of long-read and short-read data</p> <p>isomiga_novel: just the novel isoforms</p> <p>isomiga_gencode: the novel isoforms combined with all isoforms in GENCODE v38.</p> <p>Not included: GENCODE v38 - available at https://www.gencodegenes.org/human/release_38.html</p> <p><strong>Isoform coordinates (GTF)</strong></p> <p>All files bgzipped and tabixed for easy random access by IGV. {file}.gtf.gz is the Isoform list, {file}.gtf.gz.tbi is the tabix index.</p> <p><strong>Isoform sequences (FASTA)</strong></p> <p>All files gzipped. </p> <p> </p>
Fig. 5 in Study of two isoforms of lipoxygenase by kinetic assays, docking and molecular dynamics of a specialised metabolite isolated from the aerial portion of Lithrea caustica (Anacardiaceae) and its synthetic analogs
Fig. 5. Active site of molecular dynamics between 3-pentadecylcatechol (2) (A), (Z)-3-(pentadec-10′-enyl)-catechol (1) (B), and arachidonic acid with 5-hLOX and fluctuation of catechol distances during simulation time (10 ns).
Isolation of Vitamin D Binding Protein Isoforms From Human Volunteers
ClinicalTrials.gov study NCT02258035. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Mifepristone for Breast Cancer Patients With Higher Levels of Progesterone Receptor Isoform A Than Isoform B.
ClinicalTrials.gov study NCT02651844. IPD Sharing: UNDECIDED. Countries: 1. Publications: 23.
Study Comparing Two Isoforms of Vitamin D Supplements for Infants
ClinicalTrials.gov study NCT01190137. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Effects of One HIIT Session on Adiponectin Isoforms
ClinicalTrials.gov study NCT07146867. IPD Sharing: YES. Countries: 1. Publications: 1.
Measurement of Different Anti-Müllerian Hormone Isoforms in Expected Poor Responders
ClinicalTrials.gov study NCT03826888. IPD Sharing: Not stated. Countries: 1. Publications: 16.
Pyruvate Kinase Isoform M2 (PKM2) as a Possible Biomarker for Cancer
ClinicalTrials.gov study NCT01130584. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Drosophila SWR1 and NuA4 complexes are defined by DOMINO isoforms
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Data from: Toxin-resistant isoforms of Na+/K+-ATPase in snakes do not closely track dietary specialization on toads
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Data from: Altered expression of pectoral myosin heavy chain isoforms corresponds to migration status in the white-crowned sparrow (Zonotrichia leucophrys gambelii)
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Isoform specific activities of androgen receptor and its splice variants in prostate cancer cells
<p>Androgen receptor (AR) signaling continues to drive castration resistant prostate cancer (CRPC) in spite of androgen deprivation therapy (ADT). Constitutively active shorter variants of AR, lacking the ligand binding domain, are frequently expressed in CRPC and have emerged as a potential mechanism for prostate cancer to escape ADT. ARv7 and AR<sup>v567es </sup>are two of the most commonly detected variants of AR in clinical samples of advanced, metastatic prostate cancer. It is not clear if variants of AR merely act as weaker substitutes for AR or can mediate unique isoform specific activities different from AR. In this study, we employed LNCaP prostate cancer cell lines with inducible expression of ARv7 or AR<sup>v567es </sup>to delineate similarities and differences in transcriptomics, metabolomics and lipidomics resulting from the activation of AR, ARv7 or AR<sup>v567es</sup>. While the majority of target genes were similarly regulated by the action of all three isoforms, we found a clear difference in transcriptomic activities of AR versus the variants, and a few differences between ARv7 and AR<sup>v567es</sup>. Some of the target gene regulation by AR isoforms was similar in the VCaP background as well. Differences in downstream activities of AR isoforms were also evident from comparison of the metabolome and lipidome in an LNCaP model. Overall our study implies that shorter variants of AR are capable of mediating unique downstream activities different from AR and some of these are isoform specific.</p>
Data from: The role of isoforms in the evolution of cryptic coloration in Peromyscus mice
A central goal of evolutionary biology is to understand the molecular mechanisms underlying phenotypic adaptation. While the contribution of protein-coding and cis-regulatory mutations to adaptive traits has been well documented, additional sources of variation – such as the production of alternative RNA transcripts from a single gene, or isoforms – have been understudied. Here, we focus on the pigmentation gene Agouti, known to express multiple alternative transcripts, to investigate the role of isoform usage in the evolution of cryptic colour phenotypes in deer mice (genus Peromyscus). We first characterize the Agouti isoforms expressed in the Peromyscus skin and find two novel isoforms not previously identified in Mus. Next, we show that a locally adapted light-coloured population of P. maniculatus living on the Nebraska Sand Hills shows an upregulation of a single Agouti isoform, termed 1C, compared with their ancestral dark-coloured conspecifics. Using in vitro assays, we show that this preference for isoform 1C may be driven by isoform-specific differences in translation. In addition, using an admixed population of wild-caught mice, we find that variation in overall Agouti expression maps to a region near exon 1C, which also has patterns of nucleotide variation consistent with strong positive selection. Finally, we show that the independent evolution of cryptic light pigmentation in a different species, P. polionotus, has been driven by a preference for the same Agouti isoform. Together, these findings present an example of the role of alternative transcript processing in adaptation and demonstrate molecular convergence at the level of isoform regulation.
Dataset for AI-assisted processing pipeline to boost isoform detection
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Allen Brain Atlas
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International Brain Laboratory public data
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OpenNeuro
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