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Sample GSM7046015 Query DataSets for GSM7046015
Status Public on Dec 01, 2023
Title plasma, subject 009619bdT1
Sample type protein
 
Source name serum
Organism Homo sapiens
Characteristics subject id: Subj_009619bd
blood sample id: Subj_009619bdT1
Sex: Male
age: 43
days since first sample: 1
patient classification at first sample: SARS-CoV-2_Positive_Ab_Positive
covid-19 status: Positive
in_covid_aki_dataset: No
in_covid_only_dataset: Yes
instrument model: Somascan discovery platform v4
Extracted molecule protein
Extraction protocol Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.
Label NA
Label protocol As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf
 
Hybridization protocol As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf
Scan protocol As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf
Description See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.
Data processing As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model. More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics
 
Submission date Feb 15, 2023
Last update date Dec 01, 2023
Contact name Pushkala Jayaraman
E-mail(s) pushkala.jayaraman@cahn.mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Charles Bronfman Institute of Personalized Medicine
Lab AIMS Lab
Street address 1 Gustave Levy Pl
City New York
State/province New York
ZIP/Postal code 10029
Country USA
 
Platform ID GPL33128
Series (1)
GSE225349 Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Supplementary data files not provided
Processed data are available on Series record

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