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SRX9529554: GSM4914291: PC_9_RNA_TA; Homo sapiens; RNA-Seq
2 ILLUMINA (Illumina NovaSeq 6000) runs: 70M spots, 7.1G bases, 2Gb downloads

Submitted by: NCBI (GEO)
Study: Longitudinal multi-omics identifies responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories [sequencing]
show Abstracthide Abstract
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.
Sample: PC_9_RNA_TA
SAMN16829884 • SRS7736453 • All experiments • All runs
Organism: Homo sapiens
Library:
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
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). 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.
Experiment attributes:
GEO Accession: GSM4914291
Links:
Runs: 2 runs, 70M spots, 7.1G bases, 2Gb
Run# of Spots# of BasesSizePublished
SRR1308281134,434,9453.5G1Gb2020-12-16
SRR1308281235,596,8373.6G1Gb2020-12-16

ID:
12452507

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