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84 results for “HCMV”
Assembly and variant calling results of strain mixtures of HCMV
<p>The tgz files contain the assembly contigs of 10 different assemblers and variant calling results of 6 callers on the strain mixture dataset of the HCMV virus. </p>
GRAND-SLAM analysis of HCMV infection of ZAP knockout cells from Gonzalez-Perez et al., mBio 2021 (https://doi.org/10.1128/mbio.02683-20)
<p>This is the processed SLAM-seq data from Gonzalez-Perez et al., mBio 2021 (https://doi.org/10.1128/mbio.02683-20). The zip file contains the full output from the processing pipeline (including the mapped reads, the scripts to run the pipeline and the output). The json file is required if you want to start from scratch. The file sars.tsv.gz is the GRAND-SLAM output table.</p> <p><br> To generate the GRAND-SLAM output yourself, first prepare the human (ensembl v90) and the HCMV genome (EF999921). Then run:</p> <p>gedi -e Slam -double -reads sars.cit -genomic h.ens90 HCMV_TB40_BAC4 -prefix grandslam_du/zap_bac4 -plot -progress</p> <p>[Zum Verschieben anwählen und ziehen]</p> <p>To generate the cit file you have to modify the first lines in start.bash to match the paths on your file system, and then run it.</p> <p>You can also start from scratch (i.e., the json file):</p> <p> Prepare the human genome (ensembl v90), the HCMV genome (EF999921), the human rRNA sequence (U13369.1), and the Mycoplasma hominis sequence<br> Prepare the joint STAR index for the human and virus genome by calling gedi -e GenomicUtils -p -m star -g h.ens90 HCMV_TB40_BAC4<br> Modify the starindex entry in the json file to match your file system<br> Run: gedi -e Pipeline -r parallel -j zap_bac4.json rnaseq_mapping.sh report.sh grandslam.sh</p> <p>Software versions:</p> <p> gedi toolkit 1.0.2<br> GRAND-SLAM 2.0.5a<br> Trimmomatic 0.39<br> STAR version 2.5.3a</p>
Scripts reproducing the analyses of the paper "HCMV exploits STING signaling and counteracts IFN and ISG induction to facilitate infection of dendritic cells" by Costa et al
<p>This is the code to reproduce the data analyses in the manuscript "HCMV exploits STING signaling and counteracts IFN and ISG induction to facilitate infection of dendritic cells".</p> <p>Required software and packages:</p> <p>R (4.2.1)<br>circlize (0.4.15)<br>ComplexHeatmap (2.12.1)<br>cowplot (1.1.1)<br>future (1.28.0)<br>ggalluvial (0.12.5)<br>ggpubr (0.4.0)<br>ggrepel (0.9.1)<br>GSVA (1.44.5)<br>msigdbr (7.5.1)<br>patchwork (1.1.2)<br>plyr (1.8.7)<br>presto (1.0.0)<br>RColorBrewer (1.1-3)<br>reshape2 (1.4.4)<br>sctransform (0.3.5)<br>Seurat (4.2.0)<br>SeuratDisk (0.0.0.9020)<br>SeuratWrappers (0.3.1)<br>velocyto.R (0.6)</p> <p>Howto: Execute all scripts in order by first changing into the directory, and then executing the script:</p> <pre><code>cd 00_QC; Rscript 00_QC.R; cd ..</code></pre>
Diaplacental Transfer of Anti-HCMV- and Anti-VZV-immunoglobulin G (IgG) -Antibodies at Premature and Mature Newborns
ClinicalTrials.gov study NCT02689700. IPD Sharing: NO. Countries: 1. Publications: 4.
Epidemiology and Prevention of Congenital HCMV in Immune Mothers. Congenital HCMV Infection Lombardy
ClinicalTrials.gov study NCT03973359. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Efficacy Study of Human Cytomegalovirus (HCMV) Hyperimmune Globulin to Prevent Congenital HCMV Infection
ClinicalTrials.gov study NCT00881517. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Prospective, Randomized Study for Predicting Human Cytomegalovirus (hCMV) Infection Based on Baseline hCMV Specific T-cell Response in Kidney Transplant
ClinicalTrials.gov study NCT02550639. IPD Sharing: Not stated. Countries: 2. Publications: 3.
Postnatal HCMV Infection in Very Preterm Infants. Implications, Morbidity, Growth and Neurodevelopmental Outcomes.
ClinicalTrials.gov study NCT01151462. IPD Sharing: Not stated. Countries: 1. Publications: 5.
HCMV Breakthrough Infections During Letermovir Prophylaxis
ClinicalTrials.gov study NCT06339892. IPD Sharing: NO. Countries: 1. Publications: 2.
HCMV-miRNA Monitoring After Allogeneic Hematopoietic Stem Cell Transplantation Using PSTM-qPCR
ClinicalTrials.gov study NCT07210242. IPD Sharing: NO. Countries: 0. Publications: 5.
Trial to Study Anti- HCMV Therapy in Breast Cancer Patients With Progressive Intracranial Metastases and CMV Infection
ClinicalTrials.gov study NCT07383649. IPD Sharing: Not stated. Countries: 1. Publications: 14.
Viral transcriptome analysis of HCMV infected Kasumi-3 cells at early time post infection
GEO Series GSE164840. Human betaherpesvirus 5. 6 samples. Type: Expression profiling by high throughput sequencing.
Analysis of Roquin targetome during HCMV infection
GEO Series GSE132081. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing; Other.
Transcriptome analysis of HCMV infected and mock-infected Kasumi-3 cells at 24 hours post infection
GEO Series GSE164839. Human betaherpesvirus 5; Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
HCMV virus produced in different cell types induces different transcriptional responses
GEO Series GSE9578. Homo sapiens. 5 samples. Type: Expression profiling by array.
Transcriptomic analysis of neural-induced SHED cells with/without HCMV infection
GEO Series GSE182788. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
The molecular principles governing HCMV infection outcome
GEO Series GSE189581. Homo sapiens. 32 samples. Type: Expression profiling by high throughput sequencing.
Tissue Resident CD8+T cells as mediators of protective immunity in breastmilk transmission of HCMV
GEO Series GSE281566. Homo sapiens. 4 samples. Type: Expression profiling by high throughput sequencing.
Comparison of HCMV nascent and steady state transcriptomes expresssed in the Kasumi-3 latency model at early times post-infection
GEO Series GSE164843. Human betaherpesvirus 5; Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq analysis of canonical and adaptive human NK cell and CD8+ T cell subsets from HCMV seropositive donors
GEO Series GSE117614. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
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
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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.