Gene Expression Nebulas
A data portal of transcriptomic profiles across multiple species

Gene Expression Nebulas

A data portal of transcriptome profiles across multiple species

PRJCA002326: Transcriptome of patients infected with SARS-CoV-2

Source: NGDC / CRA002390
Submission Date: Mar 4 2020
Release Date: Apr 1 2020
Update Date: Apr 1 2020

Summary: RNA-seq was employed to investigate host responses to SARS-CoV-2 infection in the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) samples of COVID-19 patients.

GEN Datasets:
GEND000183
Strategy:
Species:
Tissue:
Healthy Condition:
Cell Type:
Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: -
Library Construction Protocol: One microgram of total RNAs extracted from PBMCs (Ficoll preparation) were used as input. Messenger RNAs were purified using oligo-dTs covalently coupled magnetic beads. Then, the RNAs were fragmented into small pieces by heating. First strand of cDNA was synthesized in the presence of specific chemicals to ensure that only RNAs were used as template. Double strand cDNAs were purified with Agencourt AMPure XP beads after the reaction. DNA library was constructed through end-repair, adaptor-ligation and PCR amplification. The intermediate products were size-selected after the adaptor-ligation using two rounds of Agencourt AMPure XP beads. Qualified double strand DNA library was transformed into single-stranded circular DNA library through DNA-denaturation and circularization. DNA nanoballs (DNBs) were generated from single-stranded circular DNA using rolling circle amplification (RCA). The DNBs were qualified using Qubit 2.0. Qualified DNBs were loaded on the flow cell and sequenced.; Total RNAs were extracted from BALF samples and quantified by Qubit RNA HS Assay Kit. The library preparation was performed with Trio RNA-Seq kit with AnyDeplete probe to remove human ribosomal RNAs. The resulting libraries were subject to 150 bp pair-end sequencing with an Illumina Miseq platform.
Sequencing
Molecule Type: poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward; -
Platform: ILLUMINA; BGISEQ
Instrument Model: Illumina NovaSeq 5000; Illumina MiSeq; BGISEQ-500
Strand-Specific: Specific; Unspecific
Publications
Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in COVID-19 patients.
Emerging microbes & infections . 2020-12-01 [PMID: 32228226]
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