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ShareScore release 0.9.0
Dataset results
9 results for “Sequences from human host”
Sars-Cov-2 and Mers sequences from human host with no unknown characters
<p>The datasets are organized as follows: first column, number of bases in a given sequence; second, third, fourth and fifth columns, number of bases of type A, C, G and T, respectively, in the same sequence. </p> <p><strong>1) Sars-Cov-2 dataset. </strong>This dataset contains number of bases for the complete genome sequences from a human host, with none unknown characters.<span> </span>In the NCBI database, there are about 950.000 sequences with these characteristics.</p> <p><strong>2) Restricted Sars-Cov-2 dataset:</strong> This dataset contains number of bases for the complete sequences from a human host, with no unknown characters, with 29903 bases, that is of the same length as the reference sequence NC045512.2. We obtained, from the NCBI database, about 5600 sequences with such features.</p> <p><strong>3) Mers dataset:</strong> This dataset contains number of bases for the complete sequences of about 200 complete genome sequences from a human host, with no unknown characters.</p>
Sars-Cov-2 and Mers sequences from human host with no unknown characters
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Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
<p><b>Background: </b>Viral infections are common complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT<b>)</b>. Allo-HSCT recipients<b> </b>with steroid-refractory/dependent graft-versus-host disease (GvHD) are highly immunosuppressed and are more vulnerable to infections with weakly pathogenic or commensal viruses. Here, twenty-five adult allo-HSCT recipients from 2016 to 2019 with acute or chronic steroid-refractory/dependent GvHD were enrolled in a prospective cohort of patients at Geneva University Hospitals. We performed metagenomics next-generation sequencing (mNGS) analysis using a validated viral pipeline and <i>de novo</i> analysis on pooled stored routine plasma samples collected throughout the period of intensive steroid treatment or second-line GvHD therapy to identify weakly pathogenic, commensal and unexpected viruses.</p> <p><b>Results: </b>Median duration of intensive immunosuppression was 5.1 months (IQR 5.5).<b> </b>GvHD-related mortality rate was 36%.<b> </b>mNGS analysis detected viral nucleotide sequences in 24/25 patients. Sequences of ≥3 distinct viruses were detected in 16/25 patients, <i>Anelloviridae</i> (24/25) and human pegivirus-1 (9/25) were the most prevalent. In 7/25 patients with fatal outcomes, unexpected viral sequences, not assessed by routine investigations, were identified with mNGS and confirmed by RT-PCR. These cases included usutu virus (1), rubella virus (1 vaccine-strain and 1 wild-type), novel human astrovirus (HAstV) MLB2 (1), classic HAstV (1), human polyomavirus 6 and 7 (2), cutavirus (1), and bufavirus (1).</p> <p><b>Conclusions: </b>Unexpected, opportunistic and protracted viral infections were identified in 28% of highly immunocompromised allo-HSCT recipients with steroid refractory/dependent GvHD. These identified viruses have all been previously described in humans, but have poorly understood clinical significance. Rubella virus identification raises the possibility of re-emergence from past infections or vaccinations.</p>
Unmasking viral sequences by metagenomic next-generation sequencing in adult human blood samples during steroid-refractory/dependent graft-versus-host disease
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Dual single-cell and bulk RNA sequencing reveal transcriptional profiles underlying heterogenous host-parasite interactions in human peripheral blood mononuclear cells
GEO Series GSE295224. Homo sapiens. 42 samples. Type: Expression profiling by high throughput sequencing.
Host transcriptome sequencing of FACS-sorted human induced pluripotent stem cell-derived brain endothelial cells infected with Neisseria meningitidis
GEO Series GSE126449. Homo sapiens; Neisseria meningitidis MC58. 2 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with either bradyzoites and tachyzoite of Toxoplasma gondii
GEO Series GSE125121. Toxoplasma gondii; Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
Exploring host cellular responses to SARS-CoV-2 variants using RNA sequencing of infected human airway epithelial cells
GEO Series GSE271378. Homo sapiens. 44 samples. Type: Expression profiling by high throughput sequencing.
RNA sequencing of host transcriptome of human foreskin fibroblast cells infected with Toxoplasma gondii bradyzoites, with and without myr1 (myc regulation 1)
GEO Series GSE125120. Toxoplasma gondii; Homo sapiens. 15 samples. Type: Expression profiling by high throughput sequencing.
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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.