Gene Expression Nebulas
A data portal of transcriptomic profiles analyzed by a unified pipeline across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species
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PRJNA646705

PRJNA646705: Single-cell RNA sequencing of golden hamster upper respiratory tract (nasal mucosa and trachea), lung, kidney and small intestine

Source: NCBI / GSE154564
Submission Date: Jul 16 2020
Release Date:
Update Date: Jan 04 2021

Summary: Full understanding of the pathophysiology of COVID-19 is critical for adequate treatment and development of vaccine and therapeutics. Although Golden hamster has been emerged as animal model of COVID-19, it is unknown how SARS-CoV-2 enters and infects targeted epithelial cells at molecular and cellular levels. Here, by applying single cell RNA sequencing in the upper respiratory tract, lung, kidney and intestine of golden hamster, we show that the expression profiles of host factors for SARS-CoV-2 infection in specific cell types are similar to that of human. These data can be applied to a larger investigation (data not provided here) into the expression patterns of host cell entry factors of SARS-CoV-2 in golden hamster organs

Overall Design: To investigate the expression patterns of host cell entry factors of SARS-CoV-2 in golden hamster organs. Single cells from dedicated organs were isolated and single-cell transcriptome libraries were generated

GEN Datasets:
GEND000431
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Line:
Development Stage:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: After tissue preparation and cell digestion, single-cell suspensions were processed on the 10X chromium system following the manufacturer's protocols.
Library Construction Protocol: cDNA libraries were constructed using Chromium Single cell 3' v3 Reagent Kit (10X genomics)
Sequencing
Molecule Type: rRNA- RNA
Library Source:
Library Layout: PAIRED
Library Strand: -
Platform: ILLUMINA
Instrument Model: Illumina HiSeq X Ten
Strand-Specific: -
Samples
Basic Information:
Sample Characteristic:
Biological Condition:
Experimental Variables:
Protocol:
Sequencing:
Assessing Quality:
Analysis:
Data Resource GEN Sample ID GEN Dataset ID Project ID BioProject ID Sample ID Sample Name BioSample ID Sample Accession Experiment Accession Release Date Submission Date Update Date Species Race Ethnicity Age Age Unit Gender Source Name Tissue Cell Type Cell Subtype Cell Line Disease Disease State Development Stage Mutation Phenotype Case Detail Control Detail Growth Protocol Treatment Protocol Extract Protocol Library Construction Protocol Molecule Type Library Layout Strand-Specific Library Strand Spike-In Strategy Platform Instrument Model Cell Number Reads Number Gbases AvgSpotLen1 AvgSpotLen2 Uniq Mapping Rate Multiple Mapping Rate Coverage Rate