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ShareScore release 0.9.0
Dataset results
16 results for “fluorescent reporter”
Raw data supporting "mScarlet fluorescence lifetime reports lysosomal pH quantitatively"
<p>Original dataset and processing code supporting the preprint (scientific publication) "mScarlet fluorescence lifetime reports lysosomal pH quantitatively."</p> <p>Publication Abstract: The lysosome maintains a highly acidic pH, which is critical for successful lysosomal catabolism. Lysosomal pH (pHlys) is difficult to measure because of the simultaneous need for a sensor with large dynamic range, genetic targetability, low pKa, and a quantitative readout. Here, we demonstrate that the fluorescence lifetime of the mScarlet-LAMP1 fusion protein quantitatively reports lysosomal pH, exhibiting a large dynamic range and a pKa well-tuned for the lysosome. Because fluorescence lifetime is an intrinsic property, pH measurements can be achieved in a single fluorescence channel. mScarlet-LAMP1 lifetime allows for individual lysosome-resolved recordings, a critical advance in describing and understanding pHlys heterogeneity. Using this biosensor, we quantify heterogeneity of pHlys in cultured cells at rest and over time during drug treatment. We anticipate that mScarlet-LAMP1 will enable new insights into the diversity of lysosomal physiology and ionic milieu.</p>
Dataset to manuscript entitled "Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies" submitted to Scientifc Reports
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to</strong><strong> </strong><strong><em>Scientifc Reports, </em>and entitled</strong><strong>:</strong></p> <p><strong><em>Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies</em></strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p><strong>Niusha Bagheri <sup>1</sup>, Hongjian Chen <sup>1</sup>, Mihailo Rabasovic <sup>2</sup>, Jerker Widengren <sup>1,*</sup></strong></p> <p><sup>1 </sup>Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center 106 91 Stockholm, Sweden</p> <p><sup>2 </sup>Laboratory for Biophysics, Institute of Physics Belgrade, Pregrevica 118<br>11080 Zemun-Belgrade, Serbia</p> <p>* Corresponding author (jwideng@kth.se)</p> <p><strong> </strong></p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Like most fluorescent organic molecules, these amino acids also tend to undergo transitions into dark meta-stable states, such as triplet and photo-radical states. While this may be perceived as a problem, these transitions are also highly environment-sensitive and can be used as an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, we applied the transient state monitoring (TRAST) technique, analyzing the average intensity of tyrosine emission under different excitation modulations, to characterize the photo physics of tyrosine for such readout purposes. By investigating how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), which upon calcium binding takes a more folded conformation. From these TRAST experiments, performed with 280nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.</p>
Fluorescent reporters of exocytic events
<p>TIRF imaging of Hela cells expressing tetraspanin (CD9, CD63, CD81) and v-SNARE (VAMP2, VAMP7) reporters both coupled to pHluorin, a pH-sensitive optical probe.</p> <p>Frame rate of 5Hz.<br> 488 nm laser line</p>
Data of quantitative, ratiometric dual fluorescence reporter assay at the single-cell level
<p>The data set shows the evaluation of a new dual fluorescence reporter assay using three test genes, vimentin, lamin A/C and Arp3. This fluorescence protein-based reported assay successfully predicts siRNA efficacy with high fidelity. Data include images of Hela cells transfected with Vim-T4 ad Vim-T5 knockdown contructs; images of dual fluorescence assay; data analysis for knockdown experiments, Western blotting analysis of vimentin-knockdown in Hela cells, knockdown of endogenous lamin A/C in Hela cells; quantification of lamin A/C knockdown in Hela cells; dual fluorescence assay of human vimentin genes using three plasmids; Western blotting of Arp3 knockdown in SCC9 cells.</p> <p>All files can be opened using LibreOffice or OpenOffice. Some of the ODS files have a minor problem when opening them in Excel in the Windows computers. Excel will give warning about some unreadable contents. By choosing the repair option, the file contents will be shown without changes compared to the original data. Detailed explanation is given in the “Explanation file”.</p>
Dataset for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."
<p>Plasmid sequences for "Antisense transcription from neighboring genes interferes with the expression of mNeonGreen as a functional in vivo fluorescent reporter in the chloroplast of Chlamydomonas reinhardtii."</p>
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (2)
GEO Series GSE243456. Homo sapiens. 12 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
Transcriptomic analysis of wild-type microglia isolated from fluorescent reporter mice
GEO Series GSE204751. Mus musculus. 5 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional analysis of TDC in a fluorescent reporter model
GEO Series GSE237645. Mus musculus. 9 samples. Type: Expression profiling by high throughput sequencing.
Color-flu: multi-spectral fluorescent reporter influenza viruses as powerful tools for in vivo studies
GEO Series GSE64473. Mus musculus. 15 samples. Type: Expression profiling by array.
Identification of dormant cells using a novel fluorescent reporter of RNA-polymerase II activity
GEO Series GSE147030. Mus musculus. 10 samples. Type: Expression profiling by high throughput sequencing.
A stable Netrin-1 fluorescent reporter chicken reveals cell-specific molecular signatures during optic fissure closure.
GEO Series GSE275781. Gallus gallus. 10 samples. Type: Expression profiling by high throughput sequencing.
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter
GEO Series GSE243457. Homo sapiens. 28 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens in a dual fluorescence readthrough reporter (1)
GEO Series GSE242480. Homo sapiens. 16 samples. Type: Other.
Global transcriptomic analyses of pluripotent stem cell-derived type II alveolar epithelial-like cells identified by ABCA3:GFP and SFTPCtdTomato bi-fluorescent reporters
GEO Series GSE152656. Homo sapiens. 9 samples. Type: Expression profiling by high throughput sequencing.
Genetically encoded fluorescent reporters to visualize Lewy pathology in live brain
GEO Series GSE282108. Mus musculus. 104 samples. Type: Expression profiling by high throughput sequencing.
Endogenous miRNA-200b/c activity and regulation explored by a functional dual fluorescence reporter
GEO Series GSE154429. Homo sapiens. 8 samples. Type: Expression profiling by high throughput sequencing.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.