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MB Sample ID: SA162737
Local Sample ID: | CUcovID_0107 |
Subject ID: | SU001812 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU001812 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
CUcovID_0107 | SA162737 | FL019273 | Positive | COVID_Status |
CUcovID_0107 | SA162737 | FL019273 | Male | Sex |
CUcovID_0107 | SA162737 | FL019273 | 26 | Age |
Collection:
Collection ID: | CO001805 |
Collection Summary: | Study design, participant recruitment, and clinical data capture. Research participants were recruited and consented for participation in the COVID Biobank of the University of Colorado Anschutz Medical Campus [Colorado Multiple Institutional Review Board (COMIRB) Protocol # 20-0685]. Data was generated from deidentified biospecimens and linked to demographics and clinical metadata procured through the Health Data Compass of the University of Colorado under COMIRB Protocol # 20-1700. Participants were hospitalized either at Children’s Hospital Colorado or the University of Colorado Hospital. COVID-19 status was defined by a positive PCR reaction and/or antibody test. Cohort characteristics can be found in Supp. File 1. METHOD DETAILS. Blood processing. Blood samples were collected into EDTA tubes, PAXgene RNA, and sodium heparin tubes. After centrifugation, EDTA plasma was used for MS proteomics, SOMAscan® proteomics, as well as multiplex immunoassays using MSD technology for both cytokine profiles and seroconversion assays. From sodium heparin tubes, PBMCs were obtained by the Ficoll gradient method before cryopreservation and assembly of batches for MC analysis. |
Sample Type: | Red blood cells |
Treatment:
Treatment ID: | TR001825 |
Treatment Summary: | n/a |
Sample Preparation:
Sampleprep ID: | SP001818 |
Sampleprep Summary: | Samples were thawed on ice and extracted via a modified Folch method (chloroform/methanol/water 8:4:3), which completely inactivates other coronaviruses, such as MERS-CoV. Briefly, 20 μL of sample was diluted in 130 μL of LC-MS grade water, 600 μL of ice-cold chloroform/methanol (2:1) was added, and the samples were vortexed for 10 seconds. Samples were then incubated at 4°C for 5 minutes, quickly vortexed (5 seconds), and centrifuged at 14,000 g for 10 minutes at 4°C. The top (i.e., aqueous) phase was transferred to a new tube for metabolomics analysis and flash frozen. The bottom (i.e., organic) phase was transferred to a new tube for lipidomics analysis, then dried under N2 flow. UHPLC-MS metabolomics. Analyses were performed using a Vanquish UHPLC coupled online to a Q Exactive high resolution mass spectrometer (Thermo Fisher Scientific, Bremen, Germany). Samples (10 uL per injection) were randomized and analyzed in positive and negative electrospray ionization modes (separate runs) using a 5-minute C18 gradient on a Kinetex C18 column (Phenomenex) as described (Nemkov et al., 2019). Data were analyzed using Maven (Princeton University, Princeton, NJ, USA) in conjunction with the KEGG database and an in-house standard library. |
Processing Storage Conditions: | 4℃ |
Extract Storage: | -80℃ |
Combined analysis:
Analysis ID | AN002824 | AN002825 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Vanquish | Thermo Vanquish |
Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | POSITIVE | NEGATIVE |
Units | peak area | peak area |
Chromatography:
Chromatography ID: | CH002088 |
Chromatography Summary: | After sample randomization, 10 μL of extracts were injected into a Thermo Vanquish UHPLC system (San Jose, CA, USA) and resolved on a Kinetex C18 column (150 × 2.1 mm, 1.7 μm, Phenomenex, Torrance, CA, USA) at 450 μL/min through a 5 min gradient from 5 to 95% organic solvent B (mobile phases: A = water, 0.1% formic acid; B = acetonitrile, 0.1% formic acid) in positive ion mode. Solvent gradient: 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min 95-5% B, 3-5 min hold at 5% B. |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
Column Temperature: | 45 |
Flow Gradient: | Solvent gradient: 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min 95-5% B, 3-5 min hold at 5% B |
Flow Rate: | 450 ul/min |
Solvent A: | 100% water; 0.1% formic acid |
Solvent B: | 100% acetonitrile; 0.1% formic acid |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH002089 |
Chromatography Summary: | After sample randomization, 10 μL of extracts were injected into a Thermo Vanquish UHPLC system (San Jose, CA, USA) and resolved on a Kinetex C18 column (150 × 2.1 mm, 1.7 μm, Phenomenex, Torrance, CA, USA) at 450 μL/min through a 5 min gradient from 0 to 100% phase B (phase A was 5% acetonitrile, 95% water, 1 mM ammonium acetate, phase B was 95% acetonitrile, 5% water, 0.5 mM ammonium acetate). Solvent gradient: 0-0.5 min 0% B; 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B. |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
Column Temperature: | 45 |
Flow Gradient: | Solvent gradient: 0-0.5 min 0% B; 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B. |
Flow Rate: | 450 uL/min |
Solvent A: | 5% acetonitrile/95% water; 1 mM ammonium acetate |
Solvent B: | 95% acetonitrile/5% water; 0.5 mM ammonium acetate |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS002618 |
Analysis ID: | AN002824 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). |
Ion Mode: | POSITIVE |
MS ID: | MS002619 |
Analysis ID: | AN002825 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). |
Ion Mode: | NEGATIVE |