Summary of Study ST002752
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 PR001509. The data can be accessed directly via it's Project DOI: 10.21228/M8N71K 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 | ST002752 |
| Study Title | Biomolecular condensates create phospholipid-enriched microenvironments (Part 7 - reversed phase experiment set 2) |
| Study Type | Metabolomes of in vitro synthesized condensates |
| Study Summary | Proteins and RNA are able to phase separate from the aqueous cellular environment to form sub-cellular compartments called condensates. This process results in a protein-RNA mixture that is chemically distinct from the surrounding aqueous phase. In this project we used mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and cellular metabolites and identified metabolites enriched in the condensate phase. These proteins included SARS-CoV-2 nucleocapsid, as well as low complexity domains of MED1 and HNRNPA1. In this sub-study, we examined the metabolomes of the mouse liver samples that were used to conduct the condensate metabolome experiment described above. |
| Institute | Cornell University |
| Department | Department of Pharmacology |
| Laboratory | Dr. Samie Jaffrey |
| Last Name | Dumelie |
| First Name | Jason |
| Address | 1300 York Ave, LC-524, New York City, NY |
| jdumes98@gmail.com | |
| Phone | 6465690174 |
| Submit Date | 2023-06-22 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | xml |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-07-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001509 |
| Project DOI: | doi: 10.21228/M8N71K |
| Project Title: | Biomolecular condensates create phospholipid-enriched microenvironments |
| Project Type: | Metabolomics of in vitro condensates |
| Project Summary: | Proteins and RNA are able to phase separate from the aqueous cellular environment to form sub-cellular compartments called condensates. This process results in a protein-RNA mixture that is chemically distinct from the surrounding aqueous phase. Here we use mass spectrometry to characterize the metabolomes of condensates. To test this, we prepared mixtures of phase-separated proteins and cellular metabolites and identified metabolites enriched in the condensate phase. These proteins included SARS-CoV-2 nucleocapsid, as well as low complexity domains of MED1 and HNRNPA1. |
| Institute: | Cornell University |
| Department: | Department of Pharmacology |
| Laboratory: | Dr. Samie Jaffrey |
| Last Name: | Dumelie |
| First Name: | Jason |
| Address: | 1300 York Ave, LC-524, New York City, NY |
| Email: | jdumes98@gmail.com |
| Phone: | 6465690174 |
| Funding Source: | This work was supported by the National Institutes of Health grants R35NS111631 and R01CA186702 (S.R.J.); R01AR076029, R21ES032347 and R21NS118633 (Q.C.); and NIH P01 HD067244 and support from the Starr Cancer Consortium I13-0037 (S.S.G.). |
| Publications: | Under revision |
| Contributors: | Jason G. Dumelie, Qiuying Chen, Dawson Miller, Nabeel Attarwala, Steven S. Gross and Samie R. Jaffrey1 |
Subject:
| Subject ID: | SU002859 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Input_metabolites |
|---|---|---|
| SA289474 | RP_experiment_set_2_9 | mouse liver |
| SA289475 | RP_experiment_set_2_10 | mouse liver |
| SA289476 | RP_experiment_set_2_2 | mouse liver |
| SA289477 | RP_experiment_set_2_8 | mouse liver |
| SA289478 | RP_experiment_set_2_7 | mouse liver |
| SA289479 | RP_experiment_set_2_4 | mouse liver |
| SA289480 | RP_experiment_set_2_5 | mouse liver |
| SA289481 | RP_experiment_set_2_1 | mouse liver |
| SA289482 | RP_experiment_set_2_3 | mouse liver |
| SA289473 | RP_experiment_set_2_6 | Re-run of MED1 Condensate Sample 5 (from study ST002352) |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO002852 |
| Collection Summary: | Mouse metabolites were collected from the liver of female mice using methanol extraction. After euthanizing a mouse, the liver was immediately frozen in liquid nitrogen. We then used cold 80% methanol to extract metabolites. First, 1 ml of 80% methanol was added to the liver and incubated for 10 min at -20oC. Glass beads were added to the liver and then the liver was lysed by bead-beating for 45 s using a Tissuelyser cell disrupter (Qiagen). The lysate was incubated for 10 min at -20oC and centrifuged (13200 rpm, 5 min) to separate metabolites from macromolecules. The supernatant was collected and 200 µl of 80% methanol was added to the pellet. The incubation, shaking and centrifugation steps were repeated twice to extract more metabolites from the pellet. The three supernatants were combined and centrifuged (14000 rpm, 10 min) to separate any remaining macromolecules from the metabolites. The combined supernatants were dried using a SpeedVac Concentrator (Savant, SPD131DDA) at 25oC and the dried metabolite samples were stored at -80oC. |
| Sample Type: | Liver |
| Collection Method: | 80% methanol |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002868 |
| Treatment Summary: | Metabolites were extracted from mouse livers as discussed in collection. No special treatment was performed on the mice. |
Sample Preparation:
| Sampleprep ID: | SP002865 |
| Sampleprep Summary: | Dried-down extracts were reconstituted in 150 µl 70% acetonitrile, at a relative protein concentration of ~ 2 µg/µl. These were were injected (4 µl) for LC/MS-based targeted metabolite profiling. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Combined analysis:
| Analysis ID | AN004465 | AN004466 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Agilent Model 1290 Infinity II liquid chromatography system | Agilent Model 1290 Infinity II liquid chromatography system |
| Column | Cogent Diamond Hydride (150 × 2.1 mm, 4um) | Cogent Diamond Hydride (150 × 2.1 mm, 4um) |
| MS Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Bruker Impact HD | Bruker Impact HD |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Ion abundance (max peak height) | Ion abundance (max peak height) |
Chromatography:
| Chromatography ID: | CH003351 |
| Chromatography Summary: | Chromatography of metabolites utilized reversed phase chromatography on a Agilent ZORBAX Eclipse Plus C18, 100 × 2.1 mm, 1.8 μm. Mobile phases consisted of (A) 10 mM ammonium formate with 5 μM Agilent deactivator additive in 5:3:2 water:acetonitrile:2-propanol and (B) 10 mM ammonium formate in 1:9:90 water:acetonitrile:2-propanol. Column temperature was set at 60°C and autosampler temperature was at 20°C. The flow rate was 0.4 mL/min. The following gradient was applied: 0 min, 15% B; 0-2.5 min, to 50% B; 2.5-2.6 min, to 57%, 2.6-9 min, to 70% B; 9-9.1 min, to 93% B; 9.1-11.1 min, to 96%; 11.1- 15min, 100% B; 15-20 min, 15% B. |
| Instrument Name: | Agilent Model 1290 Infinity II liquid chromatography system |
| Column Name: | Cogent Diamond Hydride (150 × 2.1 mm, 4um) |
| Column Temperature: | 60 |
| Flow Gradient: | 0 min, 15% B; 0-2.5 min, to 50% B; 2.5-2.6 min, to 57%, 2.6-9 min, to 70% B; 9-9.1 min, to 93% B; 9.1-11.1 min, to 96%; 11.1- 15min, 100% B; 15-20 min, 15% B. |
| Flow Rate: | 0.4 mL/min |
| Solvent A: | 50% water/30% acetonitrile/20% isopropanol;10 mM ammonium formate with 5 µM Agilent deactivator additive |
| Solvent B: | 1% water/9% acetonitrile/90% isopropanol;10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS004212 |
| Analysis ID: | AN004465 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The Bruker Impact II QTOF was equipped with a vacuum insulated probe heated electrospray ionization source (VIP-HESI) (Bruker Daltonics, Billerica, USA) to identify representative lipid structures using auto-MS/MS with and without scheduled precursor list fragmentation. Fragments were compared with those deposited in LIPID MAPS, HMDB and MassBank |
| Ion Mode: | POSITIVE |
| MS ID: | MS004213 |
| Analysis ID: | AN004466 |
| Instrument Name: | Bruker Impact HD |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | The Bruker Impact II QTOF was equipped with a vacuum insulated probe heated electrospray ionization source (VIP-HESI) (Bruker Daltonics, Billerica, USA) to identify representative lipid structures using auto-MS/MS with and without scheduled precursor list fragmentation. Fragments were compared with those deposited in LIPID MAPS, HMDB and MassBank. |
| Ion Mode: | NEGATIVE |
