Summary of Study ST002349
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 | ST002349 |
| Study Title | Biomolecular condensates create phospholipid-enriched microenvironments (Part 1) |
| 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. 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 |
| jdumes98@gmail.com | |
| Phone | 6465690174 |
| Submit Date | 2022-11-04 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzdata.xml |
| Analysis Type Detail | Other |
| Release Date | 2023-03-01 |
| Release Version | 2 |
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Sample Preparation:
| Sampleprep ID: | SP002597 |
| Sampleprep Summary: | Metabolites were then extracted from each fraction and the input for LC-MS as follows. First the samples were diluted in ammonium bicarbonate buffer (50 mM NH4HCO3 pH 7.5) and briefly heated (2 min, 65oC) to disrupt condensates before being added immediately to 4x volume of ice-cold 100% methanol to precipitate protein and RNA. This heating step does not appear to be necessary for extracting these metabolites and can be excluded (Extended Data Fig. 2e,g). Protein and RNA were separated from metabolites by vortexing the samples (2 min), followed by incubation at -25oC (10 min) and then centrifugation (5 min, 13,000 rpm). The supernatant was saved and the process was repeated on the pellet two more times after adding 200 µl of 80% methanol each time to the pellet. The three supernatants were combined and centrifuged (10 min, 14000 rpm) to remove any additional macromolecules. The final supernatant was collected and dried using a SpeedVac Concentrator run at 25oC. On the day of metabolite analysis, dried-down extracts were reconstituted in 150 µl 70% acetonitrile, at a relative protein concentration of ~ 2 µg/µl, and 4 µl of this reconstituted extract was injected for LC/MS-based targeted and untargeted metabolite profiling. |
| Extract Storage: | -80℃ |
