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6,617 results for “RNA Sequencing”
Single-cell RNA sequencing reveals immunosuppressive pathways associated with metastatic breast cancer
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Whole genome RNA-sequencing reveals modulation of genes related to brain disorders by Withania somnifera in human neuroblastoma SK-N-SH cells
<p>Table S1: Human reference genome based differential gene expression; Figure S1: Reactome Pathway (50 μg/mL_3h vs C_3h); Figure S2: Reactome Pathway (50 μg/mL_9h vs C_9h); Figure S3: Reactome pathway (100 μg/mL_3h vs C_3h); Figure S4: GO Dose comparison; Reactome pathway (100 μg/mL_3h vs 50 μg/mL_3h); Figure S5: GO Dose comparison; Reactome pathway (100 μg/mL_9h vs 50 μg/mL_9h); Figure S6: GO Time comparison; Reactome pathway (50 μg/mL_9h vs 50 μg/mL_3h); Figure S7: GO Time comparison; Reactome pathway (100 μg/mL_9h vs 100 μg/mL_3h); Table S2: Disease ontology analysis of 100 μg/mL_3h vs 50 μg/mL_3h WS-treated SK-N-SH cells; Table S3: Disease ontology analysis of 100 μg/mL_9h vs 50 μg/mL_9h WS-treated SK-N-SH cells; Table S4: Disease ontology analysis of 100 μg/mL_9h vs 100 μg/mL_3h WS-treated SK-N-SH cells.</p>
Spatial reconstruction of the early hepatic transcriptomic landscape after an acetaminophen overdose using single-cell RNA sequencing
<p>We leveraged single-cell RNA sequencing to understand the early molecular events that define the hepatocyte response to acetaminophen exposure at a subpopulation level. We spatially assigned hepatocytes along the portol-central vein axis by using established landmark genes. By spatially assigning the hepatocytes were were able to account for innate differences in gene expression that existed along this gradient. The excel files herein provide the full list of differentially expressed genes between key subpopulations of interest. Additionally, we classified genes as either pericentral zonated, periportal zonated, or non-zonated, the full list of genes and their spatial assignments are included in the appropriate excel file. </p>
Analysis of RNA-seq, DNA target enrichment, and Sanger nucleotide sequence data resolves deep splits in the phylogeny of cuckoo wasps (Hymenoptera: Chrysididae)
<p>The wasp family Chrysididae (cuckoo wasps, gold wasps) comprises exclusively parasitoid and kleptoparasitic species, many of which feature a stunning iridescent coloration and phenotypic adaptations to their parasitic life style. Previous attempts to infer phylogenetic relationships among the family's major lineages (subfamilies, tribes, genera) based on Sanger sequence data were insufficient to statistically resolve the monophyly and the phylogenetic position of the subfamily Amiseginae and the phylogenetic relationships among the tribes Allocoeliini, Chrysidini, Elampini, and Parnopini (Chrysidinae). Here, we present a phylogeny inferred from nucleotide sequence data of 492 nuclear single-copy genes (230,915 aligned amino acid sites) from 94 species of Chrysidoidea (representing Bethylidae, Chrysididae, Dryinidae, Plumariidae) and 45 outgroup species by combining RNA-seq and DNA target enrichment data. We find support for Amiseginae being more closely related to Cleptinae than to Chrysidinae. Furthermore, we find strong support for Allocoeliini being the sister lineage of all remaining Chrysidinae, while Elampini represent the sister lineage of Chrysidini and Parnopini. Our study corroborates results from a recent phylogenomic investigation which revealed Chrysidoidea as likely paraphyletic</p>
RNA sequencing of PET127 mutants overexpressed using the galactose inducible promoter
<p>In Saccharomyces cerevisiae, <em>PET127</em> is a mitochondrial RNA exonuclease known to interact with the mitochondrial RNA polymerase <em>RPO41</em>. The nature of the interaction between <em>PET127</em> and <em>RPO41</em> is unclear. Here, we overexpressed different <em>PET127</em> mutants for five hours utilizing the galactose inducible promoter on high-copy plasmids, collected samples, and performed RNA sequencing to understand the mitochondrial RNA landscape in each condition. The mutants tested were <em>PET127</em> lacking the nuclease activity (<em>pet127-nd</em>) and two truncated forms of <i>PET127</i>: either lacking the <em>RPO41</em> binding region (<i>pet127∆(48-215</i>)), or only containing the <i>RPO41</i> binding region (<em>pet127(1-215)</em>).</p>
RNA sequencing of nuclease dead PET127 conditions
<p><em>PET127, </em>is thought to be a mitochondrial RNA exonuclease and loss of <em>PET127</em> is thought to cause accumulation of untrimmed RNA in the mitochondria. Here we show RNA sequencing of <em>Saccharomyces cerevisiae</em> in four <em>PET127</em> conditions: <em>PET127</em> wild-type, <em>pet127∆, pet127-nd </em>(nuclease dead)/<em>pet127∆, </em>and <i>pet127-nd</i>/<i>PET127. </i>The resulting sequences show that regions of mitochondrial RNA accumulate in the <i>pet127</i><em>∆</em> background, and the RNA sequencing profile of <em>PET127</em> containing disruptive mutations in the conserved exonuclease active site mimics that of <em>pet127∆</em>. </p>
Clipped pentaloop files used for identification and characterization of RNA pentaloop sequence families
<p>This dataset includes the pentaloop structures that were clipped from PDB structures and used in the structural analysis described in Identification and Characterization of RNA Pentaloop Sequence Families</p>
Benchmarking the Autoencoder Design for Imputing Single-Cell RNA Sequencing Data
<p>This repository contains the real and synthetic datasets used in the paper "Benchmarking the Autoencoder Design for Imputing Single-Cell RNA Sequencing Data". The zip file includes three folders:</p> <p>1. overall imputation accuracy: the 12 real scRNA-seq datasets used in the evaluation of overall imputation accuracy.</p> <p>2. cell clustering: the 20 real scRNA-seq datasets with cell type labels used in the evaluation of cell clustering.</p> <p>3. DE gene: the 20 scRNA-seq syntehtic datasets with ground-truth DE genes used in the evaluation of DE gene analysis. These datasets are simulated by simulator scDesign and 20 real datasets. </p> <p> </p>
Single-cell RNA sequencing of Sox17-expressing lineages reveals distinct gene regulatory networks and dynamic developmental trajectories
<p>Two seurat objects contains single-cell RNA sequencing data that captures <em>Sox17</em>-expressing lineages during embryogenesis.</p> <p>sox17_integrated_Figure2B.rds :</p> <p>This is a seurat object that contains single-cell RNA sequencing data from integration of GFP+ cells produced from <em>Sox17<sup>GFPCre</sup></em> allele marking cells that currently express <em>Sox17</em> or short-term progeny of <em>Sox17­-</em>expressing progenitors and TdTomato+ cells produced from <em>R26<sup>LSL.TdTomato</sup></em> reporter allele in the presence of <em>Sox17<sup>GFPCre</sup></em> marking long-term progeny of <em>Sox17</em>-expressing progenitors. Inferred cell types in this seurat object reflects Figure 2B in the article.</p> <p>sox17_Prox1_endoderm_Figure5A.rds :</p> <p>This is a seurat object that contain single-cell RNA sequencing data from integration of <em>Sox17</em>- and <em>Prox1</em>-expressing endoderm dataset. Prox-1 expressing endoderm data is from the Willnow et al. <em>Nature</em>(2021). Inferred cell types in this seurat object reflects Figure 5A in the article.</p>
Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection
<p>Thi file contain results of 24 grapevines leaf samples analyzed using dsRNA-MiSeq (Illumina Miseq) and dsRNAcD sequencing (ONT nanopore), that were used in the following article ''<strong>Nanopore Sequencing of Double-Stranded RNA (dsRNA) for Plant Virus and Viroid Detection'' </strong> submitted in Frontiers in Microbiology </p>
A molecular cell atlas of the human lung from single cell RNA sequencing
<p>https://cellxgene.cziscience.com/collections/5d445965-6f1a-4b68-ba3a-b8f765155d3a</p> <p>https://www.nature.com/articles/s41586-020-2922-4</p>
Single-nucleus RNA-sequencing reveals oligodendrocytes and their progenitors as vulnerable cell types in prefrontal cortex and anterior cingulate of brains with Parkinson's disease
<p>Several prior studies have proposed the involvement of various brain regions and cell types in Parkinson's disease (PD) pathology. Here, we performed snRNA-seq on the prefrontal cortex and anterior cingulate regions from post-mortem control and PD brain tissue. We found a dramatic association of oligodendrocytes and oligodendrocyte precursor cells with PD-linked risk loci and reported several dysregulated genes and pathways, including regulation of tau-protein kinase activity, regulation of inclusion body assembly and protein processing involved in protein targeting to mitochondria.</p>
Supplementary data for paper "RNA in situ conformation sequencing reveals novel long-range RNA interactions that impact splicing"
<p>Supplementary data for paper "RNA in situ conformation sequencing reveals novel long-range RNA structures with impact on splicing".</p> <p>Data showing support for PCCR (<a href="https://www.nature.com/articles/s41467-021-22549-7">paper</a>) in RIC-seq data (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE190214">archive</a>).</p> <p> </p> <p>S1: for each supported PCCR lists numbers of experiments with inner and outer support and number of supporting reads in each experiment</p> <p>S2: for select PCCR lists supporting and non-supporting cell lines, total number of supporting reads and mean PSI in each group, and difference in mean PSI between the groups</p>
The contribution of multiplexing single cell RNA sequencing in acute myeloid leukemia
<p>Figures and supplimentary data of article : " The contribution of multiplexing single cell RNA sequencing in acute myeloid leukemia"</p>
Processed Single-cell RNA-sequencing data from adult recurrent respiratory papillomatosis
<p>.rds file (read in R) that contains processed single-cell RNA-sequencing data from 13 untreated adult recurrent respiratory papillomatosis clinical samples. The associated raw RNA sequencing data is available through The Database of Genotypes and Phenotypes (dbGaP), accession number phs003349.v1.p1. Sequences were also alsigned to a, HPV reference to allow quantification of HPV 6 or 11 gene expression. </p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 2
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
De novo nanopore sequencing overrepresents RNA modification landscape, part 3
<p>RNA modifications are critical to the functional diversity and regulatory complexity of the transcriptome. With increasing frequency, direct nanopore RNA sequencing is applied to identify RNA modifications de novo. Here, we directly compare the MS2 phage genome RNA modification profiles determined using nanopore to orthogonal LC-MS/MS assays. The results reveal very different views of the modification landscape, suggesting caution when calling new RNA modifications using nanopore alone.</p>
"Immunoregulation in Atherosclerosis: A Single-Cell RNA Sequencing Study"
ClinicalTrials.gov study NCT06860295. IPD Sharing: YES. Countries: 1. Publications: 15.
RNA Sequencing in the Framingham Heart Study Third Generation Cohort Exam 2
ClinicalTrials.gov study NCT03225183. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Discovering Early Biomarkers in Circulating Endothelial Cells for Diabetes Complications by Single Cell RNA Sequencing
ClinicalTrials.gov study NCT05169502. IPD Sharing: YES. Countries: 1. Publications: 4.
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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.
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.