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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PRJNA679331

PRJNA679331: Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [sequencing]

Source: NCBI / GSE161777
Submission Date: Nov 18 2020
Release Date:
Update Date: Dec 11 2020

Summary: In order to characterise the temporal dynamics of host response during COVID-19, we performed a longitudinal multi-omics study using a two centre German cohort of 13 patients. Bulk RNA was extracted from peripheral blood sampled at up to 5 time points per patient. At each sample point, a patient’s disease trajectory, “pseudotime”, was categorised according to clinical parameters. Both, whole transcriptome and B cell receptor sequence analysis was used to determine signatures specific to different disease trajectories. We identified coexpression modules that were associated with specific patterns across different COVID-19 disease trajectories. One module identified was related to failing interferon I response at the peak of disease severity. A second module showed biphasic upregulation of transcripts associated with erythropoiesis. Bulk BCR identified expansion of IgA+ and IgG+ cells. In sum, this study demonstrated distinct gene expression dynamics upon SARS-CoV-2 infection

Overall Design: 13 patients were sampled at days 0, 2, 7, 10, 13 and/or at discharge. 1 patient with mild disease was enrolled after recovery as a recovery control. 14 Healthy donors sampled at single time point were included as controls

GEN Datasets:
GEND000416
Strategy:
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Protocol
Growth Protocol: -
Treatment Protocol: -
Extract Protocol: Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
Library Construction Protocol: RNA sequencing libraries were prepared according to the Illumina TruSeq messenger (mRNA) sequencing protocol (TruSeq RNA Seq Library Prep Kit v2). The resulting libraries were sequenced on the NovaSeq 6000 (2× 50 bp, S2 chemistry).
Sequencing
Molecule Type: Poly(A)+ RNA
Library Source:
Library Layout: PAIRED
Library Strand: Forward
Platform: ILLUMINA
Instrument Model: Illumina NovaSeq 6000
Strand-Specific: Specific
Samples
Basic Information:
Sample Characteristic:
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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
Publications
Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19.
Immunity . 2020-11-26 [PMID: 33296687]