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Dataset results
232 results for “RNA therapeutics”
Data files: Single-cell RNA profiling of Plasmodium vivax-infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets
<p>Scripts, preprocessed count matrices, and single-cell data objects generated in <strong>“Single-cell RNA profiling of <em>Plasmodium vivax</em><em>-</em>infected hepatocytes reveals parasite- and host- specific transcriptomic signatures and therapeutic targets” </strong></p>
Beyondcell: targeting cancer therapeutic heterogeneity in single-cell RNA-seq
<p><strong><a href="https://gitlab.com/bu_cnio/Beyondcell">Beyondcell</a> </strong>is a methodology for the identification of drug vulnerabilities in single cell RNA-seq data. To this end, <strong>Beyondcell</strong> focuses on the analysis of drug-related commonalities between cells by classifying them into distinct therapeutic clusters. We have validated the tool in a population of MCF7-AA cells exposed to 500nM of bortezomib and collected at different time points: t0 (before treatment), t12, t48 and t96 (72h treatment followed by drug wash and 24h of recovery) obtained from <a href="https://www.nature.com/articles/s41586-018-0409-3"><strong><em>Ben-David U, et al., Nature, 2018</em></strong></a>. Here, you can find the integrated Seurat object obtained from this analysis. This object is meant to help users follow <strong>Beyondcell's</strong> <a href="https://gitlab.com/bu_cnio/Beyondcell/-/tree/master/tutorial/analysis_workflow">analysis workflow</a>.</p> <p> </p>
Single-cell RNA-Seq-based deconvolution of hairy cell leukemia reveals novel disease drivers and identifies DUSP1 as potential therapeutic target
<p>Microwell-based (BD Rhapsody) scRNA-seq of Hairy Cell Leukemia Patients published in </p> <blockquote> <p><strong>Single-cell RNA-Seq-based deconvolution of hairy cell leukemia reveals novel disease drivers and identifies DUSP1 as potential therapeutic target, Jan-Paul Bohn et al. Submitted.</strong></p> </blockquote> <p>The files will be made available upon publication. <br></p> <h4><strong>Description of the files</strong></h4> <ul> <li><strong>01_raw_counts: </strong>count matrices as CSV as generated by the BD Rhapsody WTA analysis pipeline</li> <li><strong>10_prepare_adata</strong>: Load BD Rhapsody WTA analysis pipeline outputs into AnnData objects and add metadata.</li> <li><strong>20_scrnaseq_qc</strong>: Use a nextflow pipeline (stored in lib/single-cell-analysis-nf) to perform threshold-based filtering of single-cell data and apply SOLO for doublet detection.</li> <li><strong>30_merge_adata</strong>: Merge samples into a single AnnData object, train a scVI model for batch effect removal, and annotate cell-types based on unsupervised clustering</li> <li><strong>40_cluster_analysis</strong>: Identify and investigate subclusters representing cell-states that go beyond the major cell-types</li> <li><strong>50_de_analysis</strong>: Generate pseudobulk and perform differential gene expression analysis using DESeq2 (based on a wrapper script stored in lib/deseq2_workflow)</li> <li><strong>70_downstream_analysis</strong>: Perform pathway analyses and generate figures for publication based on the data generated in the previous steps</li> <li><strong>containers:</strong> Conda environments used for the analysis packed up as singularity containers. </li> </ul>
Dataset related to: Therapeutic Small Interfering RNA Targeting Complement C3 in a Mouse Model of C3 Glomerulopathy
<p>The files contain all the dataset included in the manuscript divided by figures.</p> <p> </p> <p>Abstract</p> <p>Alternative pathway complement dysregulation with abnormal glomerular C3 deposits and glomerular damage is a key mechanism of pathology in C3 glomerulopathy (C3G). No disease-specific treatments are currently available for C3G. Therapeutics inhibiting complement are emerging as a potential strategy for the treatment of C3G. In this study, we investigated the effects of N-acetylgalactosamine (GalNAc) conjugated small interfering RNA (siRNA) targeting the C3 component of complement that inhibits liver C3 expression in the C3G model of mice with heterozygous deficiency of factor H (Cfh+/- mice). We showed a duration of action for GalNAc-conjugated C3 siRNA in reducing the liver C3 gene expression in Cfh+/- mice that were dosed s.c. once a month for up to 7 mo. C3 siRNA limited fluid-phase alternative pathway activation, reducing circulating C3 fragmentation and activation of factor B. Treatment with GalNAc-conjugated C3 siRNA reduced glomerular C3d deposits in Cfh+/- mice to levels similar to those of wild-type mice. Ultrastructural analysis further revealed the efficacy of the C3 siRNA in slowing the formation of mesangial and subendothelial electron-dense deposits. The present data indicate that RNA interference mediated C3 silencing in the liver may be a relevant therapeutic strategy for treating patients with C3G associated with the haploinsufficiency of complement factor H.</p>
Study to Investigate the Therapeutic Role of RNA Fragments in Platelet Production During Chemotherapy
ClinicalTrials.gov study NCT01163110. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A plastic EMP1⁺ to LGR5⁺ cell state conversion as a therapeutic bypass to KRAS-G12D inhibition in metastatic colorectal cancer [RNA-Seq]
GEO Series GSE303692. Mus musculus. 24 samples. Type: Expression profiling by high throughput sequencing.
Discovery, delineation and therapeutic targeting of a hyper-translation pathway driving cytokine release syndrome [RSK1_KO_RNA-seq]
GEO Series GSE287445. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
CXCL8/CXCR2 signaling is Enriched in Fibrotic Myeloproliferative Neoplasms and is Vulnerable to Therapeutic Inhibition [RNA-Seq]
GEO Series GSE189979. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas [RNA-Seq 2]
GEO Series GSE286565. Homo sapiens. 40 samples. Type: Expression profiling by high throughput sequencing.
Alveolar Soft Part Sarcoma is driven by ASPSCR1::TFE3-dependent and therapeutically targetable transcriptional programs [RNA-Seq]
GEO Series GSE235738. Homo sapiens. 35 samples. Type: Expression profiling by high throughput sequencing.
Whole-genome CRISPR screening identifies N-glycosylation as an essential pathway and a potential novel therapeutic target in CALR-mutant MPN (RNA-Seq).
GEO Series GSE203457. Mus musculus. 16 samples. Type: Expression profiling by high throughput sequencing.
Targeting the lineage-specific long non-coding RNA LINC01212 as an effective anti-melanoma therapeutic strategy [2]
GEO Series GSE70177. Homo sapiens. 9 samples. Type: Expression profiling by array.
RNA decay defines the therapeutic response to transcriptional perturbation in leukemia [SLAMseq THP1 RNAPII targeting]
GEO Series GSE229312. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (RNA-Seq)
GEO Series GSE124227. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Integrated analysis of MLL-AF9 AML patients and model leukemias highlights RET and other novel therapeutic targets (RNA-seq shRNA)
GEO Series GSE72041. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomic Characterization Reveals Disrupted Medium Spiny Neuron Trajectories in Huntington's Disease and Possible Therapeutic Avenues [Bulk RNA-seq treated with Cerulenin]
GEO Series GSE232647. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Identification of PRMT5 as a therapeutic target in cholangiocarcinoma [RNA-seq II]
GEO Series GSE270181. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
RNA N6-methyladenosine methyltransferase METTL3 drives NAFLD-HCC and is a therapeutic target for boosting immunotherapy [RNA-Seq]
GEO Series GSE233806. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Chemical Inhibition of Salt-Inducible Kinase as Therapeutic Strategy in Acute Myeloid Leukemia [RNA-Seq]
GEO Series GSE129862. Mus musculus; Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Enhancing Non-Small Cell Lung Cancer Treatment Utilizing Natural Killer Cell-Derived Extracellular Vesicles (NKEVS) As A Novel Adoptive Cellular Therapeutic [EV RNA]
GEO Series GSE274584. Homo sapiens. 21 samples. Type: Expression profiling by high throughput sequencing.
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.