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8 results for “CD8+ Tcells”
Atlas of virus specific CD8+ Tcells
<p>Code and Data accompanying the manuscript " "</p> <p><strong>TS logistic regression model:</strong></p> <ul> <li>TargetScape_Model_FCS_Input.zip contains the TS data in pickled format to be imported in python</li> <li>targetscape-model-paper-20221001.html contains the python code to perform data analysis, model training, testing and interpretation</li> </ul> <p><strong>TAP logistic regression model:</strong></p> <ul> <li>Generate_Pseudobulk_Markers_ADT_TAP_Cohort.R to generate candidate features by pseudo-bulking surface markers across donors.</li> <li>TAP_ParameterBenchmarking_Model_Training_Evaluation.R to perform model training and parameter benchmark.</li> <li>TAP_DiscoveryCohort_Epitopes.rds file containing a Seurat object of the TAP-Cohort.</li> <li>Cohort_Pseudobulk_ADT_Virus_markers.RDS RDS file containing the candidate markers and their fold-changes/p-values, generated by<em> Generate_Pseudobulk_Markers_ADT_TAP_Cohort.R</em></li> <li><a href="https://zenodo.org/api/files/e8452b8d-5749-4f08-be29-b9c0922a5727/Leave-one-epitope-out-TAP.R">Leave-one-epitope-out-TAP.R</a>: R script to train a model using one epitope as a validation set.</li> </ul> <p><strong>Figures related to Machine Learning approaches:</strong></p> <ul> <li>Model_Analysis_Figure_Table_Generation.R script to generate Figures 3 and Figure 4 of the main manuscript as well as corresponding Supplementary Figures</li> <li>TargetScapeModel_Feature_Importance.csv contains the regression coefficients of the model learned on TargetScape (TS) data.</li> <li>TargetScape_Cohort_Logicle.csv contains the actual data of the TS cohort after logicle transformation.</li> <li>TargetScape_Validation_Cohort_Logicle.csv contains the actual data of the TS validation cohort after logicle transformation</li> <li>TargetScape_Model_Predictions.csv contains predictions of the TS model made on the TS validation cohort</li> <li>Performance_Benchmarking_TAP.zip contains all parameter benchmarking performance files generated by the TAP model above while executing TAP_ParameterBenchmarking_Model_Training_Evaluation<em>.R.</em></li> <li>Performance_Selected_Model.txt contains model performance information on the selected TAP model</li> <li>TAP_Model_MultinomialElaNetLogRegModel_minCellsPerPatient_30_minCellsPerVirus_200_ResourcePaper.RDS contains the best model trained on TAP data.</li> <li>TAP-Validation.RDS contains the Seurat object of the TAP validation cohort.</li> </ul>
CD34 Selected Allogeneic HCT w/ Myeloablative Conditioning Plus CD8+ Memory TCell Infusion in MDS, AL and CML
ClinicalTrials.gov study NCT04151706. IPD Sharing: NO. Countries: 1. Publications: 0.
Comparison of naïve, postmitotic (CD44-lo/CD62L-hi) and effector (CD44-hi/CD62L-lo) CD8+ Tcells during BMT in GVHD mice
GEO Series GSE13743. Mus musculus. 9 samples. Type: Expression profiling by array.
Synonymous mitochondrial DNA variation impairs CD8 T cell fate via codon affinity [Tcell Culture scATAC]
GEO Series GSE216911. Homo sapiens. 2 samples. Type: Genome binding/occupancy profiling by high throughput sequencing; Other.
Gene expression analysis in naïve and vaccine (peptide vs. DC) primed pmel-1 CD8 Tcells
GEO Series GSE94538. Mus musculus. 3 samples. Type: Expression profiling by array.
CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells
GEO Series GSE189766. Mus musculus. 32 samples. Type: Expression profiling by high throughput sequencing; Other.
CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells [RNA-seq]
GEO Series GSE189592. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing.
CPEB4-mediated translational regulation in ex vivo activated CD8 Tcells [RIP-seq]
GEO Series GSE189765. Mus musculus. 20 samples. Type: Other.
ScienceDex guides
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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.