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.
8,068
datasets available to search
ShareScore release 0.7.1
Dataset results
8,068 results for “Transcriptome analysis”
Lemonade Creek, Yellowstone National Park, USA - Microbial Community Analysis - Genome and Transcriptome Data
<p>Genome and Transcriptome data used for analysis of microbial community function over a diurnal cycle in Lemonade Creek, Yellowstone National Park, USA.</p> <p> </p> <p><code>mags.tar</code> Non-redundant metagenome data (genome assemblies, predicted genes, and gene functional annotations).</p> <p> </p> <p>In each directory are the the following files:</p> <p>- <code>*.mRNA.faa</code> protein sequences of protein-coding genes</p> <p>- <code>*.mRNA.fna</code> nucleotide sequences of protein-coding genes</p> <p>- <code>*.mRNA.gff3</code> genomic location of protein-coding genes</p> <p>- <code>*.mRNA.emapper.tsv</code> eggNOG-mapper annotations for the protein-coding genes</p> <p>- <code>*.mRNA.interproscan.gff3</code> InterProScan annotations for the protein-coding genes</p> <p> </p> <p>In the <code>prokaryote</code> directory there are the following files:</p> <p>- <code>*.rRNA.fna</code> nucleotide sequences of rRNA genes</p> <p>- <code>*.rRNA.gff3</code> genomic location of rRNA genes</p> <p>- <code>*.tRNA.fna</code> nucleotide sequences of tRNA genes</p> <p>- <code>*.tRNA.gff3</code> genomic location of tRNA genes</p> <p>- <code>*.other.fna</code> nucleotide sequences of other genes (i.e., CRISPR, ncRNA, oriC, regulatory_region, repeat_region, tmRNA - if any were predicted)</p> <p>- <code>*.other.gff3</code> genomic location of other genes</p> <p> </p> <p><strong>Eukaryotes</strong></p> <p>Five MAGs from other eukaryotes that were assembled from a coassembly of the Soil samples.</p> <p> </p> <p><strong>Prokaryotes</strong></p> <p>The final dereplicated prokaryote MAGs (at 95% ID). The two <code>*stats*</code> files list the taxonomic information (from <code>GTDB-Tk</code>), completeness (from <code>CheckM</code>), and assembly stats (from the <code>stats.sh</code> script from the <code>bbmap</code> package) for each of the prokaryotic MAGs + the number of predicted protein-coding and non-protein-coding genes predicted in each MAG.</p> <p> </p> <p><strong>Viruses</strong></p> <p>The final dereplicated viral MAGs and vOTUs.</p> <p> </p> <p> </p> <p> </p> <p><code>read_mapping.tar</code> Abundance results from metagenome and metatranscriptome read mapping analysis against the non-redundant metagenome data and predicted genes (respectively). This analysis includes the cyanidiophyceae reference nuclear and organelle genomes.</p> <p> </p> <p><strong>mags</strong></p> <p>Results from <code>bbmaps</code> alignment of metagenome reads against a database of non-redudant metagenome MAGs + cyanidiophyceae reference nuclear and organelle genomes. <code>CoverM</code> was used to calculate MAG abundances.</p> <p> </p> <p><strong>genes</strong></p> <p><code>Salmon</code> abundance quantification of PolyA and RiboMinus metatranscriptome reads mapped against the predicted genes in the non-redudant metagenome MAGs + cyanidiophyceae reference nuclear and organelle genomes.</p>
Transcriptomic Analysis of Streptococcus agalactiae Periprosthetic Joint Infection
<p>Supplemental data from the study entitled "Transcriptomic Analysis of <em>Streptococcus agalactiae </em>Periprosthetic Joint Infection"</p>
Time-series transcriptome analysis identified differentially expressed genes in broiler chicken infected with mixed Eimeria species
<p>Coccidiosis caused by the <em>Eimeria</em> species is a highly problematic disease in the chicken industry. Here, we used RNA sequencing to observe the time-dependent host responses of <em>Eimeria</em>-infected chickens to examine the genes and biological functions associated with immunity to the parasite. Transcriptome analysis was performed at three time points: 4, 7, and 21 days post-infection (dpi). Based on the changes in gene expression patterns, we defined three groups of genes that showed differential expression. This enabled us to capture evidence of endoplasmic reticulum stress at the initial stage of <em>Eimeria</em> infection. Furthermore, we found that innate immune responses against the parasite were activated at the first exposure; they then showed gradual normalization. Although the cytokine-cytokine receptor interaction pathway was significantly operative at 4 dpi, its downregulation led to an anti-inflammatory effect. Additionally, the construction of gene co-expression networks enabled identification of immunoregulation hub genes and critical pattern recognition receptors after <em>Eimeria</em> infection. Our results provide a detailed understanding of the host-pathogen interaction between chicken and <em>Eimeria</em>. The clusters of genes defined in this study can be utilized to improve chickens for coccidiosis control.</p>
Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads
<p>Synthesized chemical defenses have broadly evolved across countless taxa and are important in 30 shaping evolutionary and ecological interactions within ecosystems. However, the underlying 31 genomic mechanisms by which these organisms synthesize and utilize their toxins are relatively 32 unknown. Herein, we use comparative transcriptomics to uncover potential toxin synthesizing 33 genes and pathways, as well as interspecific patterns of toxin synthesizing genes across ten 34 species of North American true toads (Bufonidae). Upon assembly and annotation of the ten 35 transcriptomes, we explored patterns of relative gene expression and possible protein-protein 36 interactions across the species to determine what genes and/or pathways may be responsible for 37 toxin synthesis. We also tested our transcriptome dataset for signatures of positive selection to 38 reveal how selection may be acting upon potential toxin producing genes. We assembled high 39 quality transcriptomes of the bufonid parotoid gland, a tissue not often investigated in other 40 bufonid related RNAseq studies. We found several genes involved in metabolic and biosynthetic 41 pathways (e.g. steroid biosynthesis, terpenoid backbone biosynthesis, isoquinoline biosynthesis, 42 glucosinolate biosynthesis) that were functionally enriched and/or relatively expressed across the 43 ten focal species that may be involved in the synthesis of alkaloid and steroid toxins, as well as 44 other small metabolic compounds that cause distastefulness in bufonids. We hope that our study 45 lays a foundation for future studies to explore the genomic underpinnings and specific pathways 46 of toxin synthesis in toads, as well as at the macroevolutionary scale across numerous taxa that 47 produce their own defensive toxins.</p>
Co-transcriptomic analysis of the maize-western corn rootworm interaction
<p>We used a maize genotype, Mp708, that is resistant to a large guild of herbivore pests to study the underlying plant defense signaling network between below and aboveground tissues. We also evaluated WCR compensatory transcriptome responses. Using RNA-seq, we profiled the transcriptome of roots and leaves that interacted with WCR infestation up to 5 days post infestation (dpi). Our results suggest that several maize defense genes were induced in roots, whereas WCR defense genes were downregulated at 5 dpi. These findings indicate a dynamic transcriptomic dialog between WCR and WCR-infested maize plants.</p>
Transcriptomic cross-species analysis of chronic liver disease reveals consistent regulation between humans and mice
<p>Data used to analyse chronic and acute liver disease in mice and human as described in <a href="https://doi.org/10.1002/hep4.1797">Holland et al. 2021</a>.</p> <p>Corresponding code is available on <a href="https://github.com/saezlab/liver-disease-atlas">GitHub</a>.</p>
Supplementary material 1 from: Graupner N, Boenigk J, Bock C, Jensen M, Marks S, Rahmann S, Beisser D (2017) Functional and phylogenetic analysis of the core transcriptome of Ochromonadales. Metabarcoding and Metagenomics 1: e19862. https://doi.org/10.3897/mbmg.1.19862
KEGG orthologous genes of the core trancriptome of the herein investigated Ochromonadales (Poteriospumella lacustris strains JBC07, JBM10, JBNZ41; Poterioochromonas malhamensis DS; Spumella vulgaris 199hm; Pedospumella encystans JBMS11) used for phylogenetic analyses.
Transcriptome data of the analysis of two isolates of the tomato pathogen Cladosporium fulvum during host interaction
<p>This dataset contains sequences of assembled transcripts from isolates Race 5 and Race 4 of the tomato pathogen Cladosporium fulvum during interaction with its host.</p> <p><strong>transcripts:</strong> Assembled transcripts in FASTA and GTF fomats. The GTF files have coordinates of the transcripts in the reference genomes of isolates Race 5 (GCA_020509005.2) and Race 4 (GCA_035196885.1). The other FASTA files include the predicted open reading frames (ORFs) in the transcripts. The nucleotide coding sequence and translated amino acid sequences of the ORFs are in separated FASTA files. In the file names isolate Race 5 is indicated with '*R5*', and isolate Race 4 is indicated with '*R4*'. Description of the files is shown below:</p> <ul> <li><code>representatives_R4_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 4.</li> <li><code>representatives_R5_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 5.</li> <li><code>representatives_R4_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 4 in the genome of Race 4.</li> <li><code>representatives_R5_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 5 in the genome of Race 5.</li> <li><code>representatives_orfs_aa_R4_diff_introns.fasta:</code> predicted protein sequences encoded in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_aa_R5_diff_introns.fasta</code>: predicted protein sequences encoded in the transcripts from isolate Race 5.</li> <li><code>representatives_orfs_cds_R4_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_cds_R5_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 5.</li> </ul> <p><strong>expression:</strong> Contains tab-separated files with the expression values (transcripts per million - TPM) of the transcripts from isolates Race 5 and Race 4 at specific time points (2, 4, 6, 8, 10, 12, and 14 dpi) during interaction with tomato. TPM values were estimated with the alignment-free method Salmon.</p>
Transcriptome analysis and functional study of phospholipase A2 in Galleria mellonella larvae lipid metabolism in response to envenomation by an ectoparasitoid, Iseropus kuwanae
<p>The file is the raw data of "Transcriptome analysis and functional study of phospholipase A2 in <em>Galleria mellonella</em> larvae lipid metabolism in response to envenomation by an ectoparasitoid, <em>Iseropus kuwanae</em>".</p>
Fig. 5 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 5 Differential transcript expression analysis. Bar charts represent the enriched molecular functions associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 4 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 4 Differential transcript expression analysis. Bar charts represent the enriched biological processes associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 2 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 2 Scheme of the methodology employed in this study. In a first approach, the reference transcriptome (workflow in grey) was assembled de novo from three distinct life cycle stages: the feeding stage alone (asexual generation; note that in young feeding stages, the buccal funnel is located inside in the trunk), the feeding stage with Prometheus larva(e) attached to its trunk (sexual generation) and the free-swimming chordoid larva. Secondly, in the differential gene expression analysis (workflow in black), only two different conditions were investigated: feeding stages with Prometheus larva(e) attached to its trunk and feeding stages alone. Finally, sequenced reads were mapped to the reference transcriptome
Fig. 6 in Transcriptome profiling of Symbion pandora (phylum Cycliophora): insights from a differential gene expression analysis
Fig. 6 Differential transcript expression analysis. Bar charts represent the enriched cellular components associated with the upregulated genes in a feeding stages with Prometheus larva(e) and b feeding stages alone
Fig. 4 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 4 Reconstructed mitochondrial DNA tree of the worldwide distributed wolves. The numbers at each node are the Bayesian posterior probabilities (right) and ML bootstrap propor- tions (left)
Fig. 3 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 3 Scatterplot of enriched KEGG pathways for DEGs between the Tibetan and lowland wolves. The enrichment factor is the ratio of the DEG number to the total gene number in the pathway. The dot size and color represent the gene number and the range of the p value respectively
Fig. 1 in Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco)
Fig. 1 Gene expression profiles of blood in Tibetan and lowland wolves. a Boxplot of the log transformed FPKM expression values across eight wolf blood samples. FPKM: fragments per kilobase of exon per million fragments. The solid horizontal line represents the median, and the box
Combined transcriptomics and metabolomics analysis reveals the mechanism behind the pollen abortion in early stage among male sterile lines of alfalfa
<p><span>This study investigates early-stage anther development in cytoplasmic male sterile (CMS) alfalfa lines (MSJN1A) compared to their isotypic maintainer line (MSJN1B). Histological analyses revealed abnormal degradation of tapetal cells post-meiosis in the CMS line. Notably, during the early mononuclear stage, the central vacuole in the microspores was absent, leading to evident pollen abortion. These findings suggest that pollen abortion in the CMS line is associated with the delayed disintegration of the tapetum and structural anomalies in microspore vacuoles.</span><span> </span><span>Non-targeted metabolomic sequencing was employed to analyze the early anther metabolites of alfalfa, identifying four hundred and one and four hundred and five metabolites in the late tetrad and early mononuclear stages, respectively. Among these, thirty-nine metabolites were consistently up-regulated, while eighty-eight were down-regulated. Differential analysis revealed forty-five and thirty-seven unique metabolites in each respective stage. These metabolites primarily featured in pathways related to energy, phenylpropane, sucrose and starch, and fatty acid metabolism. Integrated analysis demonstrated that differentially expressed genes (DEGs) and differential metabolites (DMs) were co-enriched in these pathways. Additionally, quantitative real-time PCR and physiological index analysis confirmed the down-regulation of key genes during anther development, illustrating that changes in gene regulation upstream could significantly impact downstream metabolite levels, ultimately influencing pollen fertility.</span></p>
Single-cell transcriptome analysis reveals evolving tumor microenvironment induced by immunochemotherapy in nasopharyngeal carcinoma
<p>18 bulks and 11 single-cell RNA sequencing samples from paired before anti-PD-1 contained treatment and on treatment in patients with treatment-naive high-risk metastatic locally advanced NPCs were obtained. We aim to explore the mechanism of response heterogeneity for locally advanced NPCs underwent immunochemotherapy.</p>
Global Transcriptomic Analysis of Topical Sodium Alginate Protection Against Peptic Damage in An In Vitro Model of Treatment-Resistant Gastroesophageal Reflux Disease
<p>PA= pepsin + Acid; "Sham + PA" means "Pretreatment + Treatment"</p> <p><span>Breakthrough symptoms </span>are thought to occur in roughly half of <span>all </span>gastroesophageal reflux disease (GERD) patients despite maximal acid suppression (proton pump inhibitor, PPI) therapy. Topical alginates have recently been shown to enhance mucosal defense against acid-pepsin insult during GERD. We aimed to examine potential alginate protection of transcriptomic changes in a cell culture model of PPI recalcitrant GERD. Immortalized normal-derived human esophageal epithelial cells underwent pretreatment with commercial alginate-based anti-reflux medications (Gaviscon Advance or Gaviscon Double Action), a matched-viscosity placebo control, or pH 7.4 buffer (sham) alone for 1 minute, followed by exposure to pH 6.0+pepsin or buffer alone for 3 minutes. RNA sequencing was conducted, and Ingenuity Pathway Analysis was performed with a false discovery rate of ≤0.01, and absolute fold-change of ≥<span>1.3. Pepsin-acid exposure disrupted gene expressions associated with epithelial barrier function, chromatin structure</span>, carcinogenesis, and inflammation<span>. Alginate formulations demonstrated protection by mitigating these changes and promoting extracellular matrix repair, downregulating proto-oncogenes, and enhancing tumor suppressor expression. </span>These data suggest molecular mechanisms by which alginates provide topical protection against injury during weakly acidic reflux and support a potential role for alginates in prevention of GERD-related carcinogenesis.</p>
Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression
Open the record for dataset details and reuse information.
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.