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171 results for “Reporter cells”
Data: multimodal cell tracking from systemic administration to tumour growth by combining gold nanorods and reporter genes
<p>This data set includes multispectral optoacoustic tomography images supporting an article on cell tracking (preprint: bioRxiv 199836; https://doi.org/10.1101/199836). The corresponding bioluminescence results are included too, as well as the spectra used for the multispectral processing. </p>
Case report: Papillary squamous cell carcinoma of the penis
<p><strong>Case history</strong></p> <p>62-year-old male with a verruciform tumor located in distal penis and involving glans.</p> <p> </p> <p><strong>Histologic findings</strong></p> <p>The microphotographs show an exophytic verruciform tumor mass characterized by papillomatosis, slight to moderate acanthosis, and hyperkeratosis. Papillae are complex, some with blunt and others with spiky tips. Fibrovascular are present in most but not all papillae and are irregularly shaped. Tumor base is jagged and there is a prominent stromal reaction. Neoplastic cells in papillae and infiltrative tumor nests are well to moderately differentiated (grades 1-2) and no koilocytic atypia is observed.</p> <p> </p> <p><strong>Discussion</strong></p> <p>Verruciform penile tumors comprise about one-quarter of all penile squamous cell carcinomas (SCC) and include papillary, verrucous, and warty carcinomas, as well as giant condylomas and carcinoma cuniculatum. As a group, verruciform carcinomas are characterized by the presence of papillomatosis, acanthosis, and hyperkeratosis. However, there are distinctive morphological features for each one of these tumors. For papillary SCC, the most distinguishing feature is the presence of complex papillae with irregularly shaped fibrovascular cores. Papillary carcinomas tend to be polymorphic with some areas exhibiting condylomatous papillae and others with a more verrucous-like aspect. Fibrovascular cores are readily found in the former and are scant or even absent in the latter.</p> <p>Another important clue in the differential diagnosis with other verruciform tumors is the presence of a jagged tumor-stroma interface. In verrucous and cuniculatum carcinomas the tumor front is broad-based. The absence of koilocytosis allows the distinction from warty carcinomas and giant condylomas, tumors in which koilocytes are conspicuous. HPV status may be helpful in problematic cases, since in papillary carcinomas the HPV detection rate is very low or even null. Immunohistochemistry for p16<sup>INK4a</sup> is also useful since the vast majority of papillary carcinomas do not overexpress this protein. In order for a penile tumor to be considered as p16<sup>INK4a</sup> positive all neoplastic cells should be stained. Cases like this one in which some cells stain and others do not should be regarded as negative for p16<sup>INK4a</sup> overexpression.</p> <p>The inguinal metastatic rate of penile papillary carcinomas is very low and the prognosis is good. Less than one-fifth of all patients present inguinal involvement and even in these cases the mortality rate is low. Even when tumors invade penile erectile tissues prognosis is good as long as no high-grade areas (observed in a minority of the patients) are identified.</p> <p>Clinically patients should be managed using risk-group stratification systems and taking into account histological grade, anatomical level of maximum tumor infiltration, and the presence of vascular and perineural invasion. </p> <p> </p> <p><strong>References</strong></p> <p><a href="https://www.ncbi.nlm.nih.gov/pubmed/20061934">Chaux et al. Am J Surg Pathol. 2010 34(2): 223-30</a></p> <p><a href="https://www.ncbi.nlm.nih.gov/pubmed/22641955">Chaux & Cubilla. Semin Diagn Pathol. 2012 29(2): 72-82</a></p> <p><a href="https://www.ncbi.nlm.nih.gov/pubmed/22641955">Chaux & Cubilla. Semin Diagn Pathol. 2012 29(2): 67-71</a></p>
Case report: Large-cell calcifying Sertoli cell tumor
<p><strong>Case history</strong></p> <p>21-year-old male with a painless mass in the right testicle and a prior history of cutaneous lesions.</p> <p> </p> <p><strong>Histologic findings</strong></p> <p>Figures show a proliferation composed of large, polygonal cells with ample, eosinophilic cytoplasm, round nuclei, evident nucleoli, with a trabecular, cord-like pattern of growth, associated with foci of dystrophic calcification and psammomatous bodies, within a myxoid loose stroma.</p> <p> </p> <p><strong>Discussion</strong></p> <p>Large-cell calcifying Sertoli cell tumor is an unusual morphological variant of Sertoli cell tumors composed of large polygonal Sertoli cells associated with calcification. Around one third of all cases appear in patients with the Carney or, less frequently, with the Peutz-Jeghers syndrome.</p> <p>Clinically, it presents as a small (<2 cm), painless testicular mass, which can be bilateral and multifocal in about 40% of the cases, especially in syndromic settings. In non-sporadic cases extratesticular manifestations are related to the associated syndrome, such as myxomas of the skin, soft-tissue, and heart and myxoid lesions of the breast, facial lentigines, cutaneous blue nevi, secondary Cushing syndrome due to pigmented adrenocortical nodular hyperplasia, pituitary somatotroph adenomas, and psammomatous melanotic schwannomas.</p> <p>Microscopically, solid, tubular, and cord-like growth patterns can be observed. Tumor cells are large polygonal with abundant eosinophilic, finely granular cytoplasm, vesicular nuclei with prominent nucleoli, within a myxohyaline stroma. Distinct calcifications characterized by large, laminated calcified nodule, psammoma bodies and focal ossification, and neutrophilic infiltration, can be also found.</p> <p>The presence of large tumor size (>4 cm), overt nuclear atypias, increased mitotic activity (>3 mitosis/10 HPF), necrosis, extratesticular extension, and vascular invasion are associated with clinical aggressive behavior. Malignant tumors appear in patients older than 25 years old and are usually not associated with syndromes.</p> <p>Tumor cells are positive for vimentin, S-100, EMA, melan-A, desmin, and inhibin, and focally positive for cytokeratins. The main differential diagnoses of large-cell calcifying Sertoli cell tumor include Sertoli cell and Leydig cell tumors.</p> <p>Most of the cases behave indolently, and surgical excision is the treatment of choice.</p>
Basaloid Squamous Cell Carcinoma: A Case Report
<p><strong>Background:</strong> The upper aerodigestive tract is where BSCC (basaloid squamous cell carcinoma), a rare variation of conventional SCC, is most frequently found. The hypopharynx, tonsil, supraglottic larynx, tongue (base), and head-neck regions are particularly susceptible to BSCC. Clinically, the presentation of BSCC is similar to that of conventional SCC, but it has a poor prognosis than traditional SCC. BSCC is distinguished histopathologically by a dimorphic-pattern, a distinctive basal cell component paired with a squamous component, and a squamous component. Compared to traditional SCC, the prognosis for BSCC is worse. However, clinically it shows similar features like conventional SCC which makes it difficult to diagnose. Therefore, histopathology and immunohistochemistry have a crucial role in diagnosing such tumors. We here present a case of a seventy-year male diagnosed with BSCC involving the tongue.</p> <p><strong>Keywords</strong>: Basaloid squamous cell carcinoma, dimorphic pattern, basaloid cells, comedo necrosis.</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 the publication titlted "A computational mechanics model for producing molecular assembly using molecularly woven pantographs" in the journal Cell Reports Physical Science, authored by Byeonghwa Goh and Joonmyung Choi.
<p>Dataset for the publication titlted "A computational mechanics model for producing molecular assembly using molecularly woven pantographs" in the journal Cell Reports Physical Science, authored by Byeonghwa Goh and Joonmyung Choi.</p>
Titration of ligands for the stimulation of MDA-MB-231 BRE and CAGA reporter cell lines
<p>Considerable amount of ligands will be consumed in the dual luciferase assay (DLA) which will be used for the screening of ALK2 inhibitors and off-target inhibition of ALK5 routinely. Ligands are costly to procure. In order to minimise wastage, it is important to determine the least amount of ligands needed to achieve optimal stimulation of ALK2 and ALK5. In these experiments, the activation of ALK2 and ALK5 by different concentrations of ligands in MDA-MB-231 reporter cells was analysed in Western Blot and DLA.</p>
CRISPRi with barcoded expression reporters dissects regulatory networks in human cells
<p>Genome-wide CRISPR screens have emerged as powerful tools for uncovering the genetic underpinnings of diverse biological processes. Incisive screens often depend on directly measuring molecular phenotypes, such as regulated gene expression changes, provoked by CRISPR-mediated genetic perturbations. Here, we provide quantitative measurements of transcriptional responses in human cells across genome-scale perturbation libraries by coupling CRISPR interference (CRISPRi) with barcoded expression reporter sequencing (CiBER-seq). To enable CiBER-seq in mammalian cells, we optimize the integration of highly complex, barcoded sgRNA libraries into a defined genomic context. CiBER-seq profiling of a nuclear factor kappa B (NF-κB) reporter delineates the canonical signaling cascade linking the transmembrane TNF-alpha receptor to inflammatory gene activation and highlights cell-type-specific factors in this response. Importantly, CiBER-seq relies solely on bulk RNA sequencing to capture the regulatory circuit driving this rapid transcriptional response. Our work demonstrates the accuracy of CiBER-seq and its potential for dissecting genetic networks in mammalian cells with superior time resolution.</p>
Paclitaxel, Bevacizumab and Pemetrexed in Patients With Untreated, Advanced Non-Small Cell Lung Cancer Using Web-Based Data Collection, Patient Self-Reporting of Adverse Effects and Automated Response
ClinicalTrials.gov study NCT00807573. IPD Sharing: Not stated. Countries: 1. Publications: 2.
A Study to Evaluate Participant and Healthcare Professional Reported Preference for Subcutaneous Atezolizumab Compared With Intravenous Atezolizumab Formulation in Participants With Non-Small Cell Lun
ClinicalTrials.gov study NCT05171777. IPD Sharing: YES. Countries: 12. Publications: 1.
Data from: In vivo tracking of dendritic cell using MRI reporter gene, ferritin
The noninvasive imaging of dendritic cells (DCs) migrated into lymph nodes (LNs) can provide helpful information on designing DCs-based immunotherapeutic strategies. This study is to investigate the influence of transduction of human ferritin heavy chain (FTH) and green fluorescence protein (GFP) genes on inherent properties of DCs, and the feasibility of FTH as a magnetic resonance imaging (MRI) reporter gene to track DCs migration into LNs. FTH-DCs were established by the introduction of FTH and GFP genes into the DC cell line (DC2.4) using lentivirus. The changes in the rate of MRI signal decay (R2*) resulting from FTH transduction were analyzed in cell phantoms as well as popliteal LN of mice after subcutaneous injection of those cells into hind limb foot pad by using a multiple gradient echo sequence on a 9.4 T MR scanner. The transduction of FTH and GFP did not influence the proliferation and migration abilities of DCs. The expression of co-stimulatory molecules (CD40, CD80 and CD86) in FTH-DCs was similar to that of DCs. FTH-DCs exhibited increased iron storage capacity, and displayed a significantly higher transverse relaxation rate (R2*) as compared to DCs in phantom. LNs with FTH-DCs exhibited negative contrast, leading to a high R2* in both in vivo and ex vivo T2*-weighted images compared to DCs. On histological analysis FTH-DCs migrated to the subcapsular sinus and the T cell zone of LN, where they highly expressed CD25 to bind and stimulate T cells. Our study addresses the feasibility of FTH as an MRI reporter gene to track DCs migration into LNs without alteration of their inherent properties. This study suggests that FTH-based MRI could be a useful technique to longitudinally monitor DCs and evaluate the therapeutic efficacy of DC-based vaccines.
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (2/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>2 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 1/4: <a href="http://doi.org/10.5281/zenodo.10066993">http://doi.org/10.5281/zenodo.10066993</a> (https://zenodo.org/uploads/10066993)</p><p>Upload 3/4: <a href="http://doi.org/10.5281/zenodo.10071726">http://doi.org/10.5281/zenodo.10071726</a> (https://zenodo.org/uploads/10071726)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (3/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>3 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 1/4: <a href="http://doi.org/10.5281/zenodo.10066993">http://doi.org/10.5281/zenodo.10066993</a> (https://zenodo.org/uploads/10066993)</p><p>Upload 2/4: <a href="http://doi.org/10.5281/zenodo.10069553">http://doi.org/10.5281/zenodo.10069553</a> (https://zenodo.org/uploads/10069553)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Data associated with Cell Reports publication: Dura-Bernal, Griffith, et al. 2023, "Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics" (1/4)
<p>This dataset includes experimental data used to constrain and validate the model, and model simulation output data for the following Cell Reports publication: <a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6">https://www.cell.com/cell-reports/fulltext/S2211-1247(23)01390-6</a></p><p>The source code for the associated A1 model and data analysis can be found here: <a href="https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data">https://github.com/NathanKlineInstitute/Macaque_auditory_thalamocortical_model_data</a>.</p><p>All zip files should unzipped into a parent folder called /data inside the Github repository above.</p><p><strong>Important:</strong> Due to the Zenodo size limit, this dataset is split among 4 Zenodo uploads. This is upload <strong>1 out of 4</strong>. The other 3 uploads can be found at: </p><p>Upload 2/4: <a href="http://doi.org/10.5281/zenodo.10069553">http://doi.org/10.5281/zenodo.10069553</a> (https://zenodo.org/uploads/10069553)</p><p>Upload 3/4: <a href="http://doi.org/10.5281/zenodo.10071726">http://doi.org/10.5281/zenodo.10071726</a> (https://zenodo.org/uploads/10071726)</p><p>Upload 4/4: <a href="http://doi.org/10.5281/zenodo.10072277">http://doi.org/10.5281/zenodo.10072277</a> (https://zenodo.org/uploads/10072277)</p><p>For more information please contact: salvador.dura-bernal@downstate.edu </p>
Supplemental Data for Cell Reports Physical Science article "Probing transference and field-induced polymer velocity in block copolymer electrolytes"
<p>The data and Jupyter notebook uploaded here is Supplemental Information for the article:</p><p><strong>Probing transference and field-induced polymer velocity in block copolymer electrolytes </strong></p><p>Coauthored by:</p><p>Michael D. Galluzzo, Hans-Georg Steinrück, Christopher J. Takacs, Aashutosh Mistry, Lorena S. Grundy, Chuntian Cao, Suresh Narayanan, Eric M. Dufresne, Qingteng Zhang, Venkat Srinivasan, Michael F. Toney, and Nitash P. Balsara.</p><p>Journal: Cell Reports Physical Science</p><p>Notes:</p><ul><li>This depository includes the experimental data used in Figure 2, 3, and 4 of the main text and an additional data set.</li><li>The Jupyter notebook "velocity_Echem_Data.ipynb' can be used to visualize the data in the .csv files provided in the folder 'echem' and 'XPCS_fits'.</li><li>The folder 'echem' contains the raw electrochemical data obtained from the two XPCS experiments discussed in the main text and an additional experiment set.</li><li>The folder 'XPCS_fits' contains the results of fitting the autocorrelation functions at each spatial position in the cell at each time point for the two XPCS experiments discussed in the main text and an additional experiment set. </li><li>The additional experiment included here (reffered to as Cell P in the Jupyter notebook) is not discussed in the main text, however it demonstrates that the second 'hump' in velocity (see Figure 3 and S5) that is observed after switching the direction of polarization was replicated in a separate experiment.</li></ul><p> </p>
Virtual Screening and Testing of GSK-3 Kinase Inhibitors Using human SH-SY5Y Neuronal cells Expressing Tau Folding Reporter and Mouse Hippocampal Primary Neuron Culture Under Tau Cytotoxicity
<p>Supplementary Figure S1. for IJMS</p>
Data for Cell Reports paper "Cortex-wide spontaneous activity non-linearly steers propagating sensory-evoked activity in awake mice"
<p>Datasets for Cell Reports paper "Cortex-wide spontaneous activity non-linearly steers propagating sensory-evoked activity in awake mice", including mouse cortical neural activity recording (preprocessed), behavioral recording and other analysis results during intermedia computation steps.</p>
Bioinformatics Analysis from Shaw Lab for Neault et al. Cell Reports. 2023
<p>Shaw lab data associated with <span><span>PMID: </span><strong>37716355. </strong></span></p> <p><span><strong><a href="https://pubmed.ncbi.nlm.nih.gov/?sort=date&term=Neault+M&cauthor_id=37716355">Mathieu Neault</a> et al. Cell Reports. 2023</strong></span></p> <p><span><strong>Files were copied from the NetworkBiology Server</strong></span></p>
Datasets and final TMM report for cell lines
<p>Contains the datasets and label files for cell lines, a README file describing the run settings, and TMM output files, including PSF reports for each cell line and TMM summary reports in PDF and tabular formats. </p>
Report: Culturing patient leukemic cells
<p>A summary of our culturing and immunophenotyping of primary leukemic cells from AML patients.</p>
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.