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353
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Dataset results
353 results for “mRNA-seq”
Arabidopsis thaliana circadian mRNA-seq gene expression processed tables from Romanowski et al., TPJ 2020.
<p>This dataset is an add-on for Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776) containing processed files for the circadian RNAseq data in tab delimited txt format.</p> <p><br> Here, you can the raw counts file, the normalized CPM values, and the full JTK result (without recalculated circadian phases, just the original ones). All genes with a read density > 0.05 in at least one timepoint were considered expressed. The read density is calculated as the amount of reads divided by the effective length of a gene (total reads / length). Genes rd file is also included.</p> <p>Some useful notes:<br> 1) Counts were assigned using ASpli and the AtRTDv2 annotation (34,212 genes).<br> 2) After filtering by rd we had a total of 18,503 expressed genes.<br> 3) 13,256 genes passed the QL F-tests.<br> 4) 9,127 genes were rhythmic according to JTK_cycle. </p> <p>For detailed protocols, please see Romanowski et al., TPJ 2020 (https://doi.org/10.1111/tpj.14776)</p> <p>The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-7933.</p> <p>All relevant custom r scripts are available at https://github.com/aromanowski/Circadian_rhythms_and_alternative_splicing</p>
Test data for running snakePipes : mRNA-seq workflow
<p><strong>Test files for running snakePipes workflows</strong></p> <p><strong>snakePipes</strong> are pipelines built using snakemake and python for the analysis of epigenomic datasets. Please refer to <a href="https://snakepipes.readthedocs.io/en/latest/">this link</a> for further information on snakePipes.</p> <p>This folder contains test files that can be used to run the mRNA-seq workflow under snakePipes. To test the workflow, follow the following steps : </p> <ul> <li>Download or prepare genome fasta, indices and annotations for mouse (<strong>GRCm38</strong>) genome.</li> <li>Download and install snakePipes via `conda create -n snakePipes -c mpi-ie -c bioconda -c conda-forge snakePipes`</li> <li>Update <a href="https://snakepipes.readthedocs.io/en/latest/content/running_snakePipes.html#genome-configuration-file">Genome configuration file</a> with path to indices and annotations.</li> <li>Move to this repository and run the example <strong>command.sh</strong></li> </ul>
Effect of shade and nitrogen content on Arabidopsis Col-0 and cytokinin mutants abcg14 and cypDM mRNA-seq gene expression processed tables.
<p>This dataset is an add-on for Gautrat et al., containing processed files for the mRNAseq data in tab delimited txt format.</p> <p>Here, you can obtain the raw counts file, the normalized CPM values, and the normalized logCPM values</p> <p>The RNA-seq raw data supporting the conclusions of this article have been deposited in ArrayExpress (Kolesnikov et al., 2015) at EMBL-EBI (www.ebi.ac.uk/arrayexpress), under accession numbers E-MTAB-13638.</p> <p>All relevant custom r scripts are available at https://github.com/aromanowski/shade_N_ck</p>
TCGA breast cancer (BRCA) mRNA-Seq data from GDC
<p>TCGA BRCA mRNA-seq data used in <a href="https://ocbe-uio.github.io/survomics/survomics.html">https://ocbe-uio.github.io/survomics/survomics.html</a></p>
mRNA-seq of Tgfbr2 KO CD8 T cells (d8/d15)
GEO Series GSE209598. Mus musculus. 23 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of human adipose tissue-derived mesenchymal stem/stromal cells (MSCs)
GEO Series GSE265844. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of Drosophila Ago2 mutants
GEO Series GSE51136. Drosophila melanogaster. 4 samples. Type: Expression profiling by high throughput sequencing.
Quantseq 3'mRNA-seq in Ctrl and TXNIP OE BMOL cells
GEO Series GSE244700. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Pervasive nuclear envelope ruptures precede ECM signaling and disease onset without activating cGAS-STING in Lamin-cardiomyopathy mice [mRNA-seq]
GEO Series GSE241577. Mus musculus. 46 samples. Type: Expression profiling by high throughput sequencing.
mRNA-Seq Expression profiling of human post-mortem BA9 brain tissue for Huntington's Disease and neurologically normal individuals
GEO Series GSE64810. Homo sapiens. 69 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of peripheral blood monocyte- and human pluripotent stem cell-derived macrophages
GEO Series GSE150893. Homo sapiens. 14 samples. Type: Expression profiling by high throughput sequencing.
Catalytic activity of nuclear METTL3 promotes functional m6A modifications that drive retinal development [mRNA-seq]
GEO Series GSE287484. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing.
ATAC-seq time course (in parallel to mRNA-seq time course), of wildtype C. elegans larvae sampled from 14h to 30h at 25oC [ATACseq_N2]
GEO Series GSE288867. Caenorhabditis elegans. 34 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
mRNA-Seq of male and female embyos of the honeybee (Apis mellifera)
GEO Series GSE159387. Apis mellifera. 12 samples. Type: Expression profiling by high throughput sequencing.
A small RNA pathway mediates allelic dosage in endosperm [mRNA-seq]
GEO Series GSE94786. Arabidopsis thaliana. 11 samples. Type: Expression profiling by high throughput sequencing.
Ago2 protects against diabetic cardiomyopathy via activating mitochondrial gene translation [mRNA-seq]
GEO Series GSE241911. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq of satellite cells cultured and expanded in F10 conventional medium, T cell conditional medium, and cytokine cocktail
GEO Series GSE58465. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
The metabolic response to a high-fat diet reveals obesity-prone and -resistant phenotypes in mice with distinct mRNA-seq transcriptome profiles
GEO Series GSE74804. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
Novel integrated multiomics analysis reveals Itgbl1-mediated regulation of fibrogenesis through antagonism of Tgfβ1 and IL1β signaling. (mRNA-Seq)
GEO Series GSE234270. Mus musculus. 2 samples. Type: Expression profiling by high throughput sequencing.
mRNA-Seq of head tissue from Drosophila melanogaster
GEO Series GSE20348. Drosophila melanogaster. 4 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.