Summary of Study ST001735

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001110. The data can be accessed directly via it's Project DOI: 10.21228/M8739H This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST001735
Study TitleThe COVIDome Explorer Researcher Portal (Red Blood Cells)
Study SummaryCOVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
Institute
University of Colorado Anschutz Medical Campus
Last NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2021-03-29
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-04-09
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M8739H
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001110
Project DOI:doi: 10.21228/M8739H
Project Title:The COVIDome Explorer Researcher Portal (Red blood cells)
Project Summary:COVID-19 pathology involves dysregulation of diverse molecular, cellular, and physiological processes. In order to expedite integrated and collaborative COVID-19 research, we completed multi-omics analysis of hospitalized COVID-19 patients including matched analysis of the whole blood transcriptome, plasma proteomics with two complementary platforms, cytokine profiling, plasma and red blood cell metabolomics, deep immune cell phenotyping by mass cytometry, and clinical data annotation. We refer to this multidimensional dataset as the COVIDome. We then created the COVIDome Explorer, an online researcher portal where the data can be analyzed and visualized in real time. We illustrate here the use of the COVIDome dataset through a multi-omics analysis of biosignatures associated with C-reactive protein (CRP), an established marker of poor prognosis in COVID-19, revealing associations between CRP levels and damage-associated molecular patterns, depletion of protective serpins, and mitochondrial metabolism dysregulation. We expect that the COVIDome Explorer will rapidly accelerate data sharing, hypothesis testing, and discoveries worldwide.
Institute:University of Colorado Anschutz Medical Campus
Last Name:Haines
First Name:Julie
Address:12801 E 17th Ave, Room 1303
Email:julie.haines@cuanschutz.edu
Phone:3037243339

Subject:

Subject ID:SU001812
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606

Factors:

Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id COVID_Status Sex Age
SA162670CUcovID_0037Negative Female 30
SA162671CUcovID_0094Negative Female 31
SA162672CUcovID_0079Negative Female 34
SA162673CUcovID_0028Negative Female 34
SA162674CUcovID_0027Negative Female 36
SA162675CUcovID_0017Negative Female 36
SA162676CUcovID_0039Negative Female 38
SA162677CUcovID_0038Negative Female 39
SA162678CUcovID_0006Negative Female 41
SA162679CUcovID_0063Negative Female 43
SA162680CUcovID_0095Negative Female 76
SA162681CUcovID_0044Negative Female 80
SA162682CUcovID_0086Negative Male 23
SA162683CUcovID_0081Negative Male 25
SA162684CUcovID_0084Negative Male 25
SA162685CUcovID_0093Negative Male 26
SA162686CUcovID_0091Negative Male 35
SA162687CUcovID_0004Negative Male 38
SA162688CUcovID_0051Negative Male 42
SA162689CUcovID_0052Negative Male 43
SA162690CUcovID_0083Negative Male 47
SA162691CUcovID_0031Negative Male 50
SA162692CUcovID_0073Negative Male 54
SA162693CUcovID_0105Negative Male 59
SA162694CUcovID_0048Negative Male 60
SA162695CUcovID_0023Negative Male 63
SA162696CUcovID_0076Negative Male 65
SA162697CUcovID_0064Negative Male 66
SA162698CUcovID_0072Negative Male 67
SA162699CUcovID_0097Negative Male 71
SA162700CUcovID_0082Negative Male under 20
SA162701CUcovID_0106Positive Female 21
SA162702CUcovID_0087Positive Female 21
SA162703CUcovID_0100Positive Female 23
SA162704CUcovID_0035Positive Female 23
SA162705CUcovID_0009Positive Female 25
SA162706CUcovID_0033Positive Female 29
SA162707CUcovID_0003Positive Female 29
SA162708CUcovID_0080Positive Female 35
SA162709CUcovID_0060Positive Female 38
SA162710CUcovID_0008Positive Female 39
SA162711CUcovID_0022Positive Female 39
SA162712CUcovID_0075Positive Female 41
SA162713CUcovID_0090Positive Female 43
SA162714CUcovID_0002Positive Female 44
SA162715CUcovID_0018Positive Female 45
SA162716CUcovID_0045Positive Female 46
SA162717CUcovID_0077Positive Female 49
SA162718CUcovID_0071Positive Female 49
SA162719CUcovID_0014Positive Female 53
SA162720CUcovID_0026Positive Female 53
SA162721CUcovID_0055Positive Female 54
SA162722CUcovID_0025Positive Female 56
SA162723CUcovID_0069Positive Female 56
SA162724CUcovID_0102Positive Female 57
SA162725CUcovID_0019Positive Female 60
SA162726CUcovID_0040Positive Female 61
SA162727CUcovID_0074Positive Female 61
SA162728CUcovID_0092Positive Female under 20
SA162729CUcovID_0078Positive Female under 20
SA162730CUcovID_0088Positive Female under 20
SA162731CUcovID_0024Positive Female under 20
SA162732CUcovID_0085Positive Female under 20
SA162733CUcovID_0050Positive Female under 20
SA162734CUcovID_0101Positive Male 20
SA162735CUcovID_0043Positive Male 21
SA162736CUcovID_0021Positive Male 24
SA162737CUcovID_0107Positive Male 26
SA162738CUcovID_0007Positive Male 28
SA162739CUcovID_0109Positive Male 30
SA162740CUcovID_0041Positive Male 33
SA162741CUcovID_0065Positive Male 34
SA162742CUcovID_0016Positive Male 41
SA162743CUcovID_0012Positive Male 42
SA162744CUcovID_0013Positive Male 42
SA162745CUcovID_0096Positive Male 43
SA162746CUcovID_0108Positive Male 45
SA162747CUcovID_0054Positive Male 46
SA162748CUcovID_0029Positive Male 47
SA162749CUcovID_0020Positive Male 50
SA162750CUcovID_0049Positive Male 50
SA162751CUcovID_0061Positive Male 51
SA162752CUcovID_0068Positive Male 52
SA162753CUcovID_0046Positive Male 54
SA162754CUcovID_0042Positive Male 55
SA162755CUcovID_0059Positive Male 55
SA162756CUcovID_0047Positive Male 59
SA162757CUcovID_0030Positive Male 60
SA162758CUcovID_0089Positive Male 60
SA162759CUcovID_0098Positive Male 61
SA162760CUcovID_0005Positive Male 61
SA162761CUcovID_0070Positive Male 69
SA162762CUcovID_0010Positive Male 71
SA162763CUcovID_0001Positive Male 77
SA162764CUcovID_0104Positive Male 79
SA162765CUcovID_0011Positive Male 79
SA162766CUcovID_0056Positive Male under 20
SA162767CUcovID_0036Positive Male under 20
SA162768CUcovID_0057Positive Male under 20
SA162769CUcovID_0062Positive Male under 20
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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
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