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Series GSE215865 Query DataSets for GSE215865
Status Public on Dec 06, 2022
Title Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Post-acute sequelae of SARS-CoV-2 infection are debilitating, clinically heterogeneous, and of unknown molecular etiology. A transcriptome-wide investigation was performed in acutely infected patients followed clinically into the post-acute period. Distinct gene-expression signatures of post-acute sequelae were already present in whole-blood during acute infection, with innate and adaptive immune cells implicated in different symptoms. Two clusters of sequelae exhibited divergent plasma-cell associated gene-expression patterns. In one cluster, sequelae associated with higher expression of immunoglobulin-related genes in an anti-spike antibody titer-dependent manner. In the other, sequelae associated independently of these titers with lower expression of immunoglobulin-related genes, indicating lower non-specific antibody production in subjects with these sequelae. This relationship between lower total immunoglobulins and sequelae was validated in an external cohort. Altogether, multiple etiologies of post-acute sequelae were already detectable during SARS-CoV-2 infection, directly linking these sequelae with the acute host response to the virus and providing early insights into their development.
 
Overall design Bulk RNA-seq of whole blood sampled longitudinally from hospitalized COVID-19 cases during acute infection as well as from healthy and hospitalized controls. See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data, RNA-seq QC data, and other data and metadata.
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The Mount Sinai COVID-19 Biobank Team
Web link https://www.nature.com/articles/s41591-022-02107-4
 
Contributor(s) Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Cervia C, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang Y, Nie K, Zaki N, Tuballes K, Barcessat V, Cedillo MA, Yuan D, Huckins L, Roussos P, Marron TU, Glicksberg BS, Nadkarni G, Heath JR, Gonzalez-Kozlova E, Boyman O, Kim-Schulze S, Sebra R, Merad M, Gnjatic S, Schadt EE, Charney AW, Beckmann ND
Citation(s) 36482101
Submission date Oct 16, 2022
Last update date Feb 08, 2023
Contact name Ryan Conrad Thompson
E-mail(s) rct@thompsonclan.org
Organization name Icahn School of Medicine at Mount Sinai
Department Charles Bronfman Institute for Personalized Medicine
Lab Beckmann Lab
Street address 1 Gustave L. Levy Place
City New York
State/province NY
ZIP/Postal code 10029-5674
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (1392)
GSM6643333 whole blood, subject 0028c054, sample time point T1, library prep Plate_2
GSM6643334 whole blood, subject 0028c054, sample time point T1, library prep Plate_5
GSM6643335 whole blood, subject 0028c054, sample time point T1, library prep Plate_7
Relations
BioProject PRJNA891054
SRA SRP402914

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE215865_rnaseq_logCPM_matrix.csv.gz 221.2 Mb (ftp)(http) CSV
GSE215865_rnaseq_raw_count_matrix.csv.gz 55.7 Mb (ftp)(http) CSV
GSE215865_rnaseq_voom_weight_matrix.csv.gz 220.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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