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.
37
datasets available to search
ShareScore release 0.9.0
Dataset results
37 results for “Differential expression analyses”
Paired differential gene expression and splicing analyses results of 199 baseline vs. case comparisons across 100 datasets
<p>This dataset contains results from paired differential expression and differential splicing analyses as well as gene-set over-representation analysis results for 199 baseline vs. case comparisons across 100 randomly curated datasets with accompanying metadata (<a href="https://doi.org/10.1186/s12915-023-01724-w" target="_blank" rel="noopener">article</a>).<br>All results were computed using the R package <a href="https://github.com/shdam/pairedGSEA">pairedGSEA</a>, which utilized DESeq2 (Love et al., 2014), DEXSeq (Anders et al., 2012), and fgsea (Korotkevich et al., 2019).<br>See limma results here: <a href="https://doi.org/10.5281/zenodo.8162214">https://doi.org/10.5281/zenodo.8162214</a><br><br>Each .RDS file contains a list with four objects: A 'metadata' object with the metadata of the respective raw data, a 'genes' object with gene-level differential splicing and expression results, a 'gene_set' object with over-representation results, and 'experiment' with the experiment title.<br><br>The filenames follow this pattern: "[dataset ID]_[GEO accession number]_[Manually assigned comparison title].RDS".<br><br>All datasets were obtained from a local copy of the ARCHS4 v11 database of transcript counts (Lachmann et al., 2018).</p>
R code for differential gene expression and enrichment analyses
<p>The information about the magnitude of differences in thermal plasticity both between and within populations, as well as identification of the underlying molecular mechanisms are key to understanding the evolution of thermal plasticity. In particular, genes underlying variation in the physiological response to temperature can provide raw material for selection acting on plastic traits. Using RNAseq, we investigate the transcriptional response to temperature in males and females from bulb mite populations selected for the increased frequency of one of two discrete male morphs (fighter- and scrambler-selected populations) that differ in relative fitness depending on temperature. We show that different mechanisms underlie the divergence in thermal response between fighter- and scrambler-selected populations at decreased vs. increased temperatures. Temperature decrease to 18°C was associated with higher transcriptomic plasticity of males with more elaborate armaments, as indicated by a significant selection-by-temperature interaction effect on the expression of 40 genes, 38 of which were upregulated in fighter-selected populations in response to temperature decrease. In response to 28°C, no selection-by-temperature interaction in gene expression was detected. Hence, differences in phenotypic response to temperature increase likely depended on genes associated with their distinct morph-specific thermal tolerance. Selection on males also drove gene expression patterns in females. These patterns could be associated with temperature-dependent fitness differences between females from fighter- vs. scrambler-selected populations reported in previous studies. Our study shows that selection for divergent male sexually selected morphologies and behaviors has the potential to drive divergence in metabolic pathways underlying plastic response to temperature in both sexes.</p>
Limma-voom differential expression results for GTEx CVD and MD analyses
<p>Supplementary File 5 for the paper entitled "Exploring the Impact of Cerebrovascular Disease and Major Depression on Non-diseased Human Tissue Transcriptomes" (doi: 10.3389/fgene.2021.696836).</p>
RNA-seq data of "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting Coffea arabica cultivars"
<p>This dataset represent FASTQ gziped files from the study "Transcriptome analyses of leaves reveal that hexanoic acid priming differentially regulate gene expression in contrasting <em>Coffea arabica</em> cultivars" (<a href="https://doi.org/10.3389/fsufs.2021.735893">https://doi.org/10.3389/fsufs.2021.735893</a>). Sequencing was done using an Illumina Novaseq 6000 instrument, paired-sequencing (2 X150 bp). Sample details are also available at https://www.ebi.ac.uk/ena/browser/view/ERA6282544.</p> <p> </p> <p>All filenames have the following naming scheme:</p> <p>LCS7609_DS_AAA_leafBBB_(R1 or R2).fq.gz</p> <p>AAA stands for the abbreviations:</p> <p>- CC (Coffea arabica cv Catuai control)</p> <p>- CHx (Coffea arabica cv Catuai exposed to Hexanoic acid)</p> <p>- OC (Coffea arabica cv Obatã control)</p> <p>- OHx (Coffea arabica cv Obatã exposed to Hexanoic acid)</p> <p>BBB stands for the number of biological replicate (1, 2 or 3).</p> <p> </p> <p> </p> <p> </p>
R code for differential gene expression and enrichment analyses
Open the record for dataset details and reuse information.
Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows
<p>Supplementary information files: Gene co-expression network and differential expression analyses of subcutaneous white adipose tissue reveal novel insights into the pathological mechanisms underlying ketosis in dairy cows</p>
Gene expression analyses of GSC11 cell in stem cell culture conditions or in differentiation conditions for 1, 3, or 7 days
GEO Series GSE28220. Homo sapiens. 12 samples. Type: Expression profiling by array.
Gene expression analyses in IRF8-induced monocyte differentiation
GEO Series GSE38810. Mus musculus. 6 samples. Type: Expression profiling by array.
Comparison of RNA Isolation Methods in Yeast on RNA-Seq: Implications for Differential Expression and Meta-Analyses
GEO Series GSE135430. Saccharomyces cerevisiae. 24 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive analyses of function and molecular interaction of differentially expressed non-coding RNAs and mRNA in Hantaan virus infection
GEO Series GSE133751. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species
GEO Series GSE76252. Drosophila melanogaster; Drosophila mauritiana; Drosophila simulans. 12 samples. Type: Expression profiling by high throughput sequencing.
A comprehensive and universal method for assessing the performance of differential gene expression analyses
GEO Series GSE22630. Homo sapiens. 36 samples. Type: Expression profiling by array.
Strong Correlation of Gene Counts and Differentially Expressed Genes Between a 3′ RNA-Seq and RNA Hybridisation Platform in Transcriptome Analyses from Canine Archival Tissue [RNA-Seq]
GEO Series GSE262022. Canis lupus familiaris. 10 samples. Type: Expression profiling by high throughput sequencing.
Bovine hepatic miRNAome profiling and differential miRNA expression analyses between beef steers with divergent feed efficiency phenotypes
GEO Series GSE144432. Bos taurus. 60 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Comparative gene expression analyses reveal distinct molecular signature between differentially reprogrammed cardiomyocytes
GEO Series GSE99814. Mus musculus. 34 samples. Type: Expression profiling by array.
Differential gene expression analyses after noncanonical peptide overexpression
GEO Series GSE216093. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Comprehensive analyses of function and molecular interaction of differential expressed non-coding RNAs and mRNA in Hantaan virus infection
GEO Series GSE133634. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Strong Correlation of Gene Counts and Differentially Expressed Genes Between a 3′ RNA-Seq and RNA Hybridisation Platform in Transcriptome Analyses from Canine Archival Tissue [3' RNA-Seq]
GEO Series GSE261790. Canis lupus familiaris. 25 samples. Type: Expression profiling by high throughput sequencing.
Myocardial RNA Sequence Analyses throughout the Course of Mouse Cardiac Laminopathy Identify Differential Expressions of the Key Genes for Cell Cycle Control and Mitochondrial Function
GEO Series GSE133693. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
mRNA-seq analyses for the differentially expressed genes (DEGs) among Con, NF VM-astrocytes, Ctx-astrocytes, and control Ctx-NPCs
GEO Series GSE106216. Mus musculus. 5 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.