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.
| Study ID | ST001735 |
| Study Title | The COVIDome Explorer Researcher Portal (Red Blood Cells) |
| Study 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 |
| julie.haines@cuanschutz.edu | |
| Phone | 3037243339 |
| Submit Date | 2021-03-29 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-04-09 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA162670 | CUcovID_0037 | Negative | Sex:Female | Age:30 |
| SA162671 | CUcovID_0094 | Negative | Sex:Female | Age:31 |
| SA162672 | CUcovID_0079 | Negative | Sex:Female | Age:34 |
| SA162673 | CUcovID_0028 | Negative | Sex:Female | Age:34 |
| SA162674 | CUcovID_0027 | Negative | Sex:Female | Age:36 |
| SA162675 | CUcovID_0017 | Negative | Sex:Female | Age:36 |
| SA162676 | CUcovID_0039 | Negative | Sex:Female | Age:38 |
| SA162677 | CUcovID_0038 | Negative | Sex:Female | Age:39 |
| SA162678 | CUcovID_0006 | Negative | Sex:Female | Age:41 |
| SA162679 | CUcovID_0063 | Negative | Sex:Female | Age:43 |
| SA162680 | CUcovID_0095 | Negative | Sex:Female | Age:76 |
| SA162681 | CUcovID_0044 | Negative | Sex:Female | Age:80 |
| SA162682 | CUcovID_0086 | Negative | Sex:Male | Age:23 |
| SA162683 | CUcovID_0081 | Negative | Sex:Male | Age:25 |
| SA162684 | CUcovID_0084 | Negative | Sex:Male | Age:25 |
| SA162685 | CUcovID_0093 | Negative | Sex:Male | Age:26 |
| SA162686 | CUcovID_0091 | Negative | Sex:Male | Age:35 |
| SA162687 | CUcovID_0004 | Negative | Sex:Male | Age:38 |
| SA162688 | CUcovID_0051 | Negative | Sex:Male | Age:42 |
| SA162689 | CUcovID_0052 | Negative | Sex:Male | Age:43 |
| SA162690 | CUcovID_0083 | Negative | Sex:Male | Age:47 |
| SA162691 | CUcovID_0031 | Negative | Sex:Male | Age:50 |
| SA162692 | CUcovID_0073 | Negative | Sex:Male | Age:54 |
| SA162693 | CUcovID_0105 | Negative | Sex:Male | Age:59 |
| SA162694 | CUcovID_0048 | Negative | Sex:Male | Age:60 |
| SA162695 | CUcovID_0023 | Negative | Sex:Male | Age:63 |
| SA162696 | CUcovID_0076 | Negative | Sex:Male | Age:65 |
| SA162697 | CUcovID_0064 | Negative | Sex:Male | Age:66 |
| SA162698 | CUcovID_0072 | Negative | Sex:Male | Age:67 |
| SA162699 | CUcovID_0097 | Negative | Sex:Male | Age:71 |
| SA162700 | CUcovID_0082 | Negative | Sex:Male | Age:under 20 |
| SA162701 | CUcovID_0106 | Positive | Sex:Female | Age:21 |
| SA162702 | CUcovID_0087 | Positive | Sex:Female | Age:21 |
| SA162703 | CUcovID_0100 | Positive | Sex:Female | Age:23 |
| SA162704 | CUcovID_0035 | Positive | Sex:Female | Age:23 |
| SA162705 | CUcovID_0009 | Positive | Sex:Female | Age:25 |
| SA162706 | CUcovID_0033 | Positive | Sex:Female | Age:29 |
| SA162707 | CUcovID_0003 | Positive | Sex:Female | Age:29 |
| SA162708 | CUcovID_0080 | Positive | Sex:Female | Age:35 |
| SA162709 | CUcovID_0060 | Positive | Sex:Female | Age:38 |
| SA162710 | CUcovID_0008 | Positive | Sex:Female | Age:39 |
| SA162711 | CUcovID_0022 | Positive | Sex:Female | Age:39 |
| SA162712 | CUcovID_0075 | Positive | Sex:Female | Age:41 |
| SA162713 | CUcovID_0090 | Positive | Sex:Female | Age:43 |
| SA162714 | CUcovID_0002 | Positive | Sex:Female | Age:44 |
| SA162715 | CUcovID_0018 | Positive | Sex:Female | Age:45 |
| SA162716 | CUcovID_0045 | Positive | Sex:Female | Age:46 |
| SA162717 | CUcovID_0077 | Positive | Sex:Female | Age:49 |
| SA162718 | CUcovID_0071 | Positive | Sex:Female | Age:49 |
| SA162719 | CUcovID_0014 | Positive | Sex:Female | Age:53 |
| SA162720 | CUcovID_0026 | Positive | Sex:Female | Age:53 |
| SA162721 | CUcovID_0055 | Positive | Sex:Female | Age:54 |
| SA162722 | CUcovID_0025 | Positive | Sex:Female | Age:56 |
| SA162723 | CUcovID_0069 | Positive | Sex:Female | Age:56 |
| SA162724 | CUcovID_0102 | Positive | Sex:Female | Age:57 |
| SA162725 | CUcovID_0019 | Positive | Sex:Female | Age:60 |
| SA162726 | CUcovID_0040 | Positive | Sex:Female | Age:61 |
| SA162727 | CUcovID_0074 | Positive | Sex:Female | Age:61 |
| SA162728 | CUcovID_0092 | Positive | Sex:Female | Age:under 20 |
| SA162729 | CUcovID_0078 | Positive | Sex:Female | Age:under 20 |
| SA162730 | CUcovID_0088 | Positive | Sex:Female | Age:under 20 |
| SA162731 | CUcovID_0024 | Positive | Sex:Female | Age:under 20 |
| SA162732 | CUcovID_0085 | Positive | Sex:Female | Age:under 20 |
| SA162733 | CUcovID_0050 | Positive | Sex:Female | Age:under 20 |
| SA162734 | CUcovID_0101 | Positive | Sex:Male | Age:20 |
| SA162735 | CUcovID_0043 | Positive | Sex:Male | Age:21 |
| SA162736 | CUcovID_0021 | Positive | Sex:Male | Age:24 |
| SA162737 | CUcovID_0107 | Positive | Sex:Male | Age:26 |
| SA162738 | CUcovID_0007 | Positive | Sex:Male | Age:28 |
| SA162739 | CUcovID_0109 | Positive | Sex:Male | Age:30 |
| SA162740 | CUcovID_0041 | Positive | Sex:Male | Age:33 |
| SA162741 | CUcovID_0065 | Positive | Sex:Male | Age:34 |
| SA162742 | CUcovID_0016 | Positive | Sex:Male | Age:41 |
| SA162743 | CUcovID_0012 | Positive | Sex:Male | Age:42 |
| SA162744 | CUcovID_0013 | Positive | Sex:Male | Age:42 |
| SA162745 | CUcovID_0096 | Positive | Sex:Male | Age:43 |
| SA162746 | CUcovID_0108 | Positive | Sex:Male | Age:45 |
| SA162747 | CUcovID_0054 | Positive | Sex:Male | Age:46 |
| SA162748 | CUcovID_0029 | Positive | Sex:Male | Age:47 |
| SA162749 | CUcovID_0020 | Positive | Sex:Male | Age:50 |
| SA162750 | CUcovID_0049 | Positive | Sex:Male | Age:50 |
| SA162751 | CUcovID_0061 | Positive | Sex:Male | Age:51 |
| SA162752 | CUcovID_0068 | Positive | Sex:Male | Age:52 |
| SA162753 | CUcovID_0046 | Positive | Sex:Male | Age:54 |
| SA162754 | CUcovID_0042 | Positive | Sex:Male | Age:55 |
| SA162755 | CUcovID_0059 | Positive | Sex:Male | Age:55 |
| SA162756 | CUcovID_0047 | Positive | Sex:Male | Age:59 |
| SA162757 | CUcovID_0030 | Positive | Sex:Male | Age:60 |
| SA162758 | CUcovID_0089 | Positive | Sex:Male | Age:60 |
| SA162759 | CUcovID_0098 | Positive | Sex:Male | Age:61 |
| SA162760 | CUcovID_0005 | Positive | Sex:Male | Age:61 |
| SA162761 | CUcovID_0070 | Positive | Sex:Male | Age:69 |
| SA162762 | CUcovID_0010 | Positive | Sex:Male | Age:71 |
| SA162763 | CUcovID_0001 | Positive | Sex:Male | Age:77 |
| SA162764 | CUcovID_0104 | Positive | Sex:Male | Age:79 |
| SA162765 | CUcovID_0011 | Positive | Sex:Male | Age:79 |
| SA162766 | CUcovID_0056 | Positive | Sex:Male | Age:under 20 |
| SA162767 | CUcovID_0036 | Positive | Sex:Male | Age:under 20 |
| SA162768 | CUcovID_0057 | Positive | Sex:Male | Age:under 20 |
| SA162769 | CUcovID_0062 | Positive | Sex:Male | Age:under 20 |
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 |
