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13,587 results for “specification”
Stage-specific embryonic antigen 4 is a specific marker for high-efficient enrichment of porcine SSCs
GEO Series GSE142410. Sus scrofa. 3 samples. Type: Expression profiling by high throughput sequencing.
A hominoid-specific signaling axis setting the tempo of synaptic maturation
GEO Series GSE246002. Mus musculus. 5 samples. Type: Genome binding/occupancy profiling by high throughput sequencing.
SIRT1 activation attenuates the cardiac dysfunction induced by endothelial cell-specific deletion of CRIF1
<p>Figure 1 (a) SIRT1 mRNA levels in the heart tissues were quantified using qPCR. (b) SIRT1 deacetylase activity in heart homogenates. (c) SIRT1 protein expression in the heart tissues were determined by western blotting. α-tubulin was used as the internal control. Densitometric analysis of SIRT1 protein levels is shown. All data are presented as means ± SEM of three independent experiments. *p < 0.05 vs. WT mice. #p < 0.05 vs. CRIF1 EKO mice.</p>
Systems pharmacology dissection of cell specific cholesterol regulation mechanisms
<p>Documentation of codes used for modeling cholesterol regulation in the manuscript "Systems pharmacology dissection of cell specific cholesterol regulation mechanisms"</p>
The non-telomeric evolutionary trajectory of TRF2 in zebrafish reveals its specific roles in neurodevelopment and aging
<p>The figures of publication: <strong>The non-telomeric evolutionary trajectory of TRF2 in zebrafish</strong></p> <p><strong>reveals its specific roles in neurodevelopment and aging</strong></p>
Supplemental Tables for: "A toolbox for class I HDACs reveals isoform specific roles in gene regulation and protein acetylation"
<p>Supplemental Table 1 - Supplement to Figure 3 and 4: MS shotgun experiment</p> <p>Supplemental Table 2 - Supplement to Figure S3: Targeted proteomics approach</p> <p>Supplemental Table 3 - Supplement to Figure 5 and S4: Gene expression analysis </p>
Supplemental Material for 'Global Soil Moisture Estimation based on GPM IMERG Data using a Site Specific Adjusted Antecedent Precipitation Index'
<p>This repository hosts all supplemental material for the publication:</p> <p><em>TBD</em></p>
SYSTACT CyTOF dataset associated with Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study
<p>This dataset contains all the raw mass cytometry (CyTOF) fcs files associated with Pogorelov et al. 'Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study', <em>Nature Communications</em>, 2024, in Press. The dataset contains all the raw fcs files generated by CyTOF analysis of 199 time-series samples including ~200 million of deeply characterized immune cells, either from patients with insect-venom allergy or patients with pollen allergy following allergen-specific immunotherapy (AIT) or from healthy controls (HC), who did not receive any AIT or other immunotherapy. As specified in the manuscript, we sampled different individuals up to seven times (0h, 8h, 24h, Day 7, Week 2, Week 6 and Week 12) over a three-month period. All the samples from insect-venom allergy patients are stored in the zipper folder called "Venom" and all the samples from pollen allergy patients are in the zipper folder called "Pollen" while all the samples from HC are placed in the zipper folder called "Control". We also provide the following annotation files (metadata) to help the readers to better understand, validate and re-analyze our immunological dataset.</p> <p>1, In addition to the Supplementary Tables in our manuscript, we also attached one Word table file mapping the 36 specific metal isotypes and the specific Ab target markers.</p> <p>2, The Excel file with the list of 199 samples, showing the correct group and time point information (of note, the manually input sample information in the file name might be wrong for some samples). The correct time point information is in the column "Timepoint Detail" and "Timepoint Final".</p> <p>Associated with these raw fcs files, our processed results of all the CyTOF data are deposited in another webpage. Our large-scale interactive interlinked immunological Data resource (i3Dare) allows investigators to more effectively explore or reuse our immunological datasets of each immune subset from each participant at each time point (please refer to <a href="https://public.tableau.com/app/profile/lihpublicdata/viz/i3Dare_SYSTACT_Database/SYSTACTHome">https://public.tableau.com/app/profile/lihpublicdata/viz/i3Dare_SYSTACT_Database/SYSTACTHome</a>). OF note, to further protect privacy, the pseudoIDs within groups in i3Dare were re-labelled again. </p> <p><strong>Please read the accompanying information/metadata files, our main manuscript and Supplementary Information, our processed data on the i3Dare webpage and the published Source Data together with the raw fcs files in order to reproduce our published results.</strong></p>
Bacteria-Specific Features Selection for Enhanced Antimicrobial Peptide Activity Predictions Using Machine-Learning Methods
<p>We developed a new computational approach that allowed us to train several supervised machine-learning models using a specific set of data associated with peptides targeting E. coli bacteria. LASSO regression and Support Vector Machine techniques have been utilized to select, among more than 1500 physio-chemical descriptors, the most important features that can be used to classify a peptide as antimicrobial or ineffective against E. coli. We then performed the classification of active versus inactive AMPs using the Support Vector classifiers, Logistic Regression, and Random Forest methods. This computational study allows us to make recommendations of how to design more efficient anti-bacterial drug therapies.</p>
Allantoic fluid metabolome reveals specific metabolic signatures in chicken lines different for their muscle glycogen content
<p>Nutrient availability in eggs can affect early metabolic orientation in birds. In chickens divergently selected on the <em>Pectoralis major</em> ultimate pH, a proxy for muscle glycogen stores, characterization of the yolk and amniotic fluid revealed a different nutritional environment. The present study aimed to assess indicators of embryo metabolism in pHu lines using allantoic fluids (compartment storing nitrogenous waste products and metabolites), collected at days 10, 14 and 17 of embryogenesis and characterized by 1H-NMR spectroscopy. Analysis of metabolic profiles revealed a significant stage effect, with an enrichment in metabolites at the end of incubation, and an increase in interindividual variability during development. OPLS-DA analysis discriminated the two lines. The allantoic fluid of pHu- was richer in carbohydrates, intermediates of purine metabolism and derivatives of tryptophan-histidine metabolism, while formate, branched-chain amino acids, Krebs cycle intermediates and metabolites from different catabolic pathways were more abundant in pHu+. In conclusion, the characterization of the main nutrient sources for embryos and now allantoic fluids provided an overview of the <em>in ovo</em> nutritional environment of pHu lines. Moreover, this study revealed the establishment, as early as day 10 of embryo development, of specific metabolic signatures in the allantoic fluid of pHu+ and pHu- lines</p>
RNAseq for "Merkel cell polyomavirus-specific and CD39+CLA+ CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma"
<p>MCC bulk RNA seq data (BAM) from sorted CD9 T cell populations (from PBMC).</p> <p>CD39neg: CD39– CD8 T cells</p> <p>CD39pos: CD39+CLA–CD103– CD8 T cells</p> <p>CLA: CD39+CLA+ CD8 T cells</p> <p>CD103: CD39+CLA–CD103+ CD8 T cells</p>
TCRseq for "Merkel cell polyomavirus-specific and CD39+CLA+ CD8 T cells as blood-based predictive biomarkers for PD-1 blockade in Merkel cell carcinoma"
<p>MCC bulk TCR seq data (fastq) from sorted CD8 T cell populations (from PBMC) and tumor.</p> <p>CD39neg: CD39– CD8 T cells</p> <p>CD39pos: CD39+CLA–CD103– CD8 T cells</p> <p>CLA: CD39+CLA+ CD8 T cells</p> <p>CD103: CD39+CLA–CD103+ CD8 T cells</p>
Bulk RNA seq - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>Bulk RNA seq data for Figure 1A performed in HT-29 cells</p> <p>triplicates for each condition: shCTRL (SHC1/2/3) & shLEPRE-1#5 (LS1/2/3)</p>
SILAC - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>Mass spec data SILAC for supplementary Figure 1A</p> <p>sheets related with this study are:<br> 2(H)+2(L) - shCTRL "heavy" vs shELP3 "light"<br> 4(H)+4(L) - shCTRL "heavy" vs shCTRL "light"</p> <p> </p>
single cell RNA seq cDNA - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>cDNA of single cell RNA seq for Figure 8A and supplementary Figure 7A</p> <p>small intestine epithelial cells from P3H1 WT and cKO mice </p> <p>3 mice per genotype and 2 biological replicates per mouse labelled by Cell Multiplexing Oligo</p> <p>Cell Multiplexing Oligo information and explanation can be found in DOI: https://doi.org/10.5281/zenodo.8207395</p>
single cell RNA seq cell plex and explanation - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>Cell Multiplexing Oligo information and explanation of single cell RNA seq for Figure 8A and supplementary Figure 7A</p> <p>small intestine epithelial cells from P3H1 WT and cKO mice </p> <p>3 mice per genotype and 2 biological replicates per mouse labelled by Cell Multiplexing Oligo</p> <p>cDNA of single cell RNA seq can be found in DOI: https://doi.org/10.5281/zenodo.8191820</p>
Dataset I related to the publication: "Designing common and specific scaffolds against two component histidine kinases: Structural insights from inhibitors of ATP binding domains"
<p>Dataset I related to the publication: "Designing common and specific scaffolds against two component histidine kinases: Structural insights from inhibitors of ATP binding domains"</p>
A novel methodology to determine the specific heat capacity of lithium-ion batteries
Open the record for dataset details and reuse information.
BiP hydroxyproline MS - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>Mass Spec data for Figure 10C</p> <p>identification of hydroxyproline at Proline 142 of BiP </p>
LEPRE-1 interactome MS - prolyl hydroxylation of BiP potentiates UPR signaling and regulates Paneth/goblet cell fate specification
<p>Mass Spec data for Figure 3C</p> <p>LEPRE-1 interactome</p>
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
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.