Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
49
datasets available to search
ShareScore release 0.9.0
Dataset results
49 results for “spatially targeted”
The spatial and temporal dynamics of the nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans [ncRNA-seq]
GEO Series GSE118428. Caenorhabditis elegans. 2 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Salmonella typhimurium targets distal colonocytes to trigger infection [Spatial Transcriptomics]
GEO Series GSE290762. Mus musculus. 4 samples. Type: Other.
Full-length target sequences of GeoMx Digital Spatial Profiling probes reveal that gene-promiscuity predicts probe sensitivity to EDTA tissue decalcification
GEO Series GSE272995. Homo sapiens. 96 samples. Type: Other.
Spatial transcriptomics reveals distinct and conserved tumor core and edge architectures that predict survival and targeted therapy response
GEO Series GSE208253. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockad
GEO Series GSE300293. Mus musculus. 19 samples. Type: Other.
Spatial hepatocyte plasticity of gluconeogenic gene expression and gluconeogenic activity during the metabolic transitions between fed, fasted and starvation states [targeted scRNA-seq]
GEO Series GSE263419. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain
GEO Series GSE182127. Mus musculus. 7 samples. Type: Expression profiling by high throughput sequencing.
Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Spatial Transcriptomics by 10X Visium]
GEO Series GSE270975. Mus musculus. 4 samples. Type: Other.
Precision targeting of beta-catenin induces tumor reprogramming and immunity in hepatocellular cancers [Spatial Transcriptomics by Resolve Biosciences Molecular Cartography]
GEO Series GSE270708. Mus musculus. 11 samples. Type: Other.
Potent anti-tumor immunity and reversal of CD8 T cell exhaustion by spatially and functionally targeting Treg cells in the tumor microenvironment
<p>1×10<sup>6</sup> of splenic GFP<sup>+</sup> Tregs were purified from WT (n=4) and KO mice (n=4) via FACS isolation. RNA was extracted using RNeasy Micro Kit (Qiagen) following its standard protocol and RNA degradation and contamination was monitored on 1% agarose gels. For RNA sequencing, libraries were prepared using NEBNext® Ultra TM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. All samples were prepared at the same time and sequenced on the same lane. Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data in FASTQ format were processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. All the downstream analyses were based on the clean data with high quality. Reference mouse genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl). Paired-end clean reads were mapped against the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software. FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM (Reads Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene. The FPKM gene expression matrix, R code, DEG list, and targeted gene list are uploaded in this project.</p>
A Spatial Analysis of Hotspots and Targeted Injection Settings Pilot Intervention for HIV Prevention Among People Who Inject Drugs
ClinicalTrials.gov study NCT05769023. IPD Sharing: YES. Countries: 1. Publications: 0.
Enhanced Spatial Targeting in ECT Utilizing FEAST
ClinicalTrials.gov study NCT04099342. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Single-cell and spatial transcriptomics analysis of tobacco-associated lung adenocarcinoma development, and in response to targeting inflammation alone or in combination with immune checkpoint blockad
GEO Series GSE300288. Mus musculus. 31 samples. Type: Expression profiling by high throughput sequencing.
Integrative single-cell and spatial transcriptomic analyses identify a pathogenic cholangiocyte niche and TNFRSF12A as therapeutic target for biliary atresia
GEO Series GSE176189. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing; Other.
CDK8 remodels the tumor microenvironment to resist the therapeutic efficacy of targeted KRASG12D inhibition in pancreatic ductal adenocarcinoma (spatial)
GEO Series GSE269680. Mus musculus. 15 samples. Type: Expression profiling by high throughput sequencing.
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [protein levels]
GEO Series GSE163529. Homo sapiens. 330 samples. Type: Other.
Spatial dynamics of the tumor microenvironment associated with emerging resistance to targeted therapy in EGFR-mutated non–small cell lung cancer
GEO Series GSE288758. Homo sapiens. 2 samples. Type: Other.
The spatial and temporal dynamics of the nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans
GEO Series GSE118429. Caenorhabditis elegans. 14 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Mapping spatial organization and genetic cell state regulators to target immune evasion in ovarian cancer
<p>This collection of data accompanies the study: <a href="https://www.nature.com/articles/s41590-024-01943-5">Yeh, Aguirre, Laveroni <em>et al.</em> <strong>Mapping spatial organization and genetic cell-state regulators to target immune evasion in ovarian cancer. </strong>(2024). </a><em><strong><a href="https://www.nature.com/articles/s41590-024-01943-5">Nature Immunology</a>.</strong></em> Files are provided in the form of RObjects (extension .rds) or tabulated data (extension .csv) to reproduce the results and figures provided in the paper via the the R programming environment using Code provided <a href="https://github.com/Jerby-Lab/HGSC_SpatialPerturbational">here</a>. </p> <p> </p> <p>Data collected and processed and published as a part of this study of tubo-ovarian high grade serous carcinoma (HGSC) includes: </p> <ul> <li>~<strong>2.5 million single cell spatial transcriptomics profiles</strong> from <strong>130 HGSC tumors</strong> of <strong>94 patients</strong></li> <li>Matching de-identified <strong>clinical annotations</strong> and clinical outcomes.</li> <li>Matching <strong>targeted genomic data</strong> from the bulk tumor tissues.</li> <li><strong>Perturb-seq CRISPR knockout</strong> data in ovarian cancer cells in monoculture and co-culture with Natural Killer (NK) cells.</li> </ul> <p>The spatial transcriptomics, Perturb-Seq, and matched H&E (Hematoxylin & Eosin, where available) are also provided via the Single Cell Portal with an <strong>interactive interface</strong> (<a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2640/hgsc-spatial-cohort-discovery-dataset">SCP2640</a>, <a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2641/hgsc-spatial-cohort-validation-1-dataset">SCP2641</a>, <a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2650/hgsc-spatial-cohort-validation-2-dataset">SCP2650</a>, <a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2644/hgsc-spatial-cohort-test-1-dataset">SCP2644</a>, <a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2646/hgsc-spatial-cohort-test-2-dataset">SCP2646</a>, <a href="https://singlecell.broadinstitute.org/single_cell/study/SCP2707/hgsc-spatial-study-perturb-seq">SCP2707</a>).</p> <p>The collection also includes previously published data that was analyzed and used in this study to examine the generalizability of the findings, evaluate immunotherapy predictors, and for data-driven experimental design.</p> <p>The SeuratObj.zip contains six SeuratObjects matching the five spatial transcriptomcs datasets (Discovery, Validation 1, Validation 2, Test 1 and Test 2) and Perturb-Seq data.</p> <p>The Yeh2024.zip file includes the study's data and additional datasets/results to reproduce the study's figures. A detailed description of the files included in the repository is provided in `README.txt` and `README.xlsx`</p>
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [gene expression levels]
GEO Series GSE162911. Homo sapiens; blank sample. 784 samples. Type: Expression profiling by high throughput sequencing; Other.
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.