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4,276 results for “transcription factors”
Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells [RNA-seq]
GEO Series GSE264707. Homo sapiens. 6 samples. Type: Expression profiling by high throughput sequencing.
Co-regulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers
GEO Series GSE50762. Mus musculus. 15 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing.
Transmission of stimulus-induced epigentic changes through cell division are coupled to changes in transcription factor activity
GEO Series GSE225855. Mus musculus. 376 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
The transcription factor ETS1 is a master regulator of human NK cell differentiation
GEO Series GSE124104. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
DNA bendability regulates transcription factor binding to nucleosomes [MNase-seq]
GEO Series GSE293024. synthetic construct. 8 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis
GEO Series GSE156047. Setaria viridis. 26 samples. Type: Expression profiling by high throughput sequencing; Other.
Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity
GEO Series GSE53348. synthetic construct. 2064 samples. Type: Other.
Critical Role of STAT5 Transcription Factor Tetramerization for Cytokine Responses and Normal Immune Function
GEO Series GSE36890. Mus musculus. 68 samples. Type: Expression profiling by array; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing.
Quantitative modeling of transcription factor binding specificities using DNA shape
GEO Series GSE59845. Homo sapiens. 3 samples. Type: Genome binding/occupancy profiling by array.
Interplay between transcription factors and DNA methylation - Appendix files
<p>This includes three appendix files for Lin, Xiaoxuan's Ph.D. thesis, Interplay between Transcription Factors and DNA Methylation.</p>
Data from: Tc-MYBPA an Arabidopsis TT2-like transcription factor and functions in the regulation of proanthocyanidin synthesis in Theobroma cacao
Background: The flavan-3-ols catechin and epicatechin, and their polymerized oligomers, the proanthocyanidins (PAs, also called condensed tannins), accumulate to levels of up to 15 % of the total weight of dry seeds of Theobroma cacao L. These compounds have been associated with several health benefits in humans. They also play important roles in pest and disease defense throughout the plant. In Arabidopsis, the R2R3 type MYB transcription factor TT2 regulates the major genes leading to the synthesis of PA. Results: To explore the transcriptional regulation of the PA synthesis pathway in cacao, we isolated and characterized an R2R3 type MYB transcription factor MYBPA from cacao. We examined the spatial and temporal gene expression patterns of the Tc-MYBPA gene and found it to be developmentally expressed in a manner consistent with its involvement in PAs and anthocyanin synthesis. Functional complementation of an Arabidopsis tt2 mutant with Tc-MYBPA suggested that it can functionally substitute the Arabidopsis TT2 gene. Interestingly, in addition to PA accumulation in seeds of the Tc-MYBPA expressing plants, we also observed an obvious increase of anthocyanidin accumulation in hypocotyls. We observed that overexpression of the Tc-MYBPA gene resulted in increased expression of several key genes encoding the major structural enzymes of the PA and anthocyanidin pathway, including DFR (dihydroflavanol reductase), LDOX (leucoanthocyanidin dioxygenase) and BAN (ANR, anthocyanidin reductase). Conclusion: We conclude that the Tc-MYBPA gene that encodes an R2R3 type MYB transcription factor is an Arabidopsis TT2 like transcription factor, and may be involved in the regulation of both anthocyanin and PA synthesis in cacao. This research may provide molecular tools for breeding of cacao varieties with improved disease resistance and enhanced flavonoid profiles for nutritional and pharmaceutical applications.
A Systems Approach to Measuring the Binding Energy Landscapes of Transcription Factors
<p>A major goal of systems biology is to predict the function of biological networks. Although network topologies have been successfully determined in many cases, the quantitative parameters governing these networks generally have not. Measuring affinities of molecular interactions in high-throughput format remains problematic, especially for transient and low-affinity interactions. We describe a high-throughput microfluidic platform that measures such properties on the basis of mechanical trapping of molecular interactions. With this platform we characterized DNA binding energy landscapes for four eukaryotic transcription factors; these landscapes were used to test basic assumptions about transcription factor binding and to predict their in vivo function.</p>
Data from: Discovery of BbX transcription factor in the patagonian blennie: Exploring expression changes following combined bacterial and thermal stress exposure
<p>Abstract:</p><p>High-Mobility Group (HMG) proteins are involved in different processes such as transcription, replication, DNA repair, and immune response. The role of HMG proteins in the immune response of fish has been studied mainly for HMGB1, where its expression can be induced by the stimulation of viral/bacterial PAMPs and can act as a proinflammatory mediator and as a global regulator of transcription in response to temperature. However, for BbX this role remains to be discovered. In this work, we identified the BbX of <i>E. maclovinus</i> and evaluated the temporal expression levels after simultaneous challenge with <i>P. salmonis</i> and thermal stress. Phylogenetic analysis does not significantly deviate from the expected organismal relationships suggesting orthologous relationships and that BbX was present in the common ancestor of the group. BbX mRNA expression levels were very high in the intestinal tissue of <i>E. maclovinus </i>(foregut, midgut, and hindgut). Nevertheless, the protein levels analyzed by WB showed the highest levels of BbX protein in the liver (constitutive expression). On the other hand, the mRNA expression levels of BbX in the liver of <i>E. maclovinus</i> injected with<i> P. salmonis</i> and subjected to thermal stress showed an increase at days 16 and 20 in all treatments applied at 12 °C and 18 °C. Meanwhile, the protein levels quantified by WB showed a statistically significant increase in the HMG-Bbx at all experimental times (4, 8, 12, 16, and 20 dpi). However, at 4 dpi the HMG-Bbx protein levels were much higher than the other days evaluated. The results suggest that BbX protein may be implicated in the response mechanism to temperature and bacterial stimulation in the foregut, midgut, hindgut, and liver, according to our findings at the level of mRNA and protein. Furthermore, our WB analysis suggests an effect of <i>P. salmonis</i> on the expression of this protein that can be observed in condition C+ 12 °C compared to C- 12 °C. Then, there is an effect of temperature that can be evidenced in the condition AM 18 °C and SM 18 °C, compared to AB 18 °C and SB 18 °C at 4, 8, and 12 dpi. We found not differences in the levels of this protein if the thermal stress is achieved through acclimatization or shock. More research is necessary to clarify the importance of this type of HMG in the immune response and thermal tolerance in fish.</p>
Putative Looping Factor ZNF143/ZFP143 is an Essential Transcriptional Regulator with No Looping Function
<h1>Overview</h1> <p>This repository contains all the raw fastSPT, FRAP, absolute abundance quantification data, and DESeq2 outputs associated with “Putative Looping Factor ZNF143/ZFP143 is an Essential Transcriptional Regulator with No Looping Function”. </p> <h1>Cell lines, conditions, and experiments</h1> <p>This repository has data for the following experiments, cell lines, and conditions. </p> <p><strong>fastSPT</strong> tracks and <strong>FRAP</strong> quantification for:</p> <ul> <li>Histone H2B</li> <li>Halo-NLS</li> <li>CTCF C87</li> <li>Clone D untreated</li> <li>Clone D ∆ZFP143 (2-4h)</li> <li>Clone A ZFP143 untreated</li> <li>Clone A ZFP143 ∆CTCF (2-4h)</li> <li>Clone B ZFP143 untreated</li> <li>Clone B ZFP143 ∆CTCF (2-4h)</li> </ul> <p><strong>FRAP</strong> quantification for:</p> <ul> <li>Clone A CTCF untreated</li> <li>Clone A CTCF ∆ZFP143 (2-4h)</li> <li>Clone B CTCF untreated</li> <li>Clone B CTCF ∆ZFP143 (2-4h)</li> <li>WT mESC pDNN13 transfection</li> <li>WT mESC pDNN14 transfection</li> <li>WT mESC pDNN15 transfection</li> </ul> <p><strong>DESeq2</strong> outputs for:</p> <ul> <li>Clone A/B ∆ZFP143 vs untreated PRO-seq</li> <li>Clone A/B ∆CTCF vs untreated PRO-seq</li> <li>Clone A/B ∆ZFP143/∆CTCF vs untreated PRO-seq</li> <li>Clone D ∆ZFP143 vs untreated PRO-seq</li> </ul> <p><strong>Other files</strong>:</p> <ul> <li>ZFP143 abundance quantification</li> <li>The parameters used for tracking (<em>tracking_config.toml</em>)</li> <li>The parameters used to get nuclear masks for fastSPT data (<em>masking_params.csv</em>)</li> </ul>
alignment of homeodomains of transcription factors of the ANTP family
<p>protein sequence alignement of HD domain used to build the tree concerning ANTP transcription factors provided in supplementary files.</p>
Data presented in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression"
<p>Here you can find the data supporting the conclusions in "Short tandem repeats bind transcription factors to tune eukaryotic gene expression." The accompanying code repository can be found at https://doi.org/10.5281/zenodo.8161422.</p>
Association Between Tendon-related Transcription Factor and Ultrasound Images and Shoulder Function
ClinicalTrials.gov study NCT04502134. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Virus Early Transcription Factor (VETF) Multicenter Phototherapy Protocol
ClinicalTrials.gov study NCT00525395. IPD Sharing: Not stated. Countries: 1. Publications: 0.
H3K9me blocks transcription factor activity in differentiated cells to ensure tissue integrity [CUT&RUN; ChICseq]
GEO Series GSE167166. Caenorhabditis elegans. 6 samples. Type: Other.
Transcription factors SP5 and SP8 drive primary cilia formation in mammalian embryos [scRNA-seq]
GEO Series GSE293888. Mus musculus. 4 samples. Type: Expression profiling by high throughput sequencing.
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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.