Summary of Study ST001822
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 PR001151. The data can be accessed directly via it's Project DOI: 10.21228/M8XH6Q 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 | ST001822 |
| Study Title | The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei |
| Study Summary | Metabolic changes following two days of RBP42 knockdown was investigated using a targeted metabolomics approach, designed to capture intermediary metabolites in central carbon metabolism including glycolytic intermediates, TCA compounds, amino acids, nucleotides and derivatives, were obtained using hydrophilic interaction liquid chromatography (HILIC) separation method coupled with mass spectrometry run in negative ionization mode |
| Institute | Rutgers University |
| Last Name | Das |
| First Name | Anish |
| Address | Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ 07103 |
| dasak@njms.rutgers.edu | |
| Phone | 9739723978 |
| Submit Date | 2021-06-07 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2021-06-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001151 |
| Project DOI: | doi: 10.21228/M8XH6Q |
| Project Title: | The RNA-binding protein RBP42 regulates cellular energy metabolism in mammalian-infective Trypanosoma brucei |
| Project Summary: | Metabolic changes following two days of RBP42 knockdown was investigated using a targeted metabolomics approach, designed to capture intermediary metabolites in central carbon metabolism including glycolytic intermediates, TCA compounds, amino acids, nucleotides and derivatives, were obtained using hydrophilic interaction liquid chromatography (HILIC) separation method coupled with mass spectrometry run in negative ionization mode. |
| Institute: | Rutgers University |
| Last Name: | Das |
| First Name: | Anish |
| Address: | Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers-New Jersey Medical School, Newark, NJ 07103 |
| Email: | dasak@njms.rutgers.edu |
| Phone: | 9739723978 |
Subject:
| Subject ID: | SU001899 |
| Subject Type: | Cultured cells |
| Subject Species: | Trypanosoma brucei brucei |
| Taxonomy ID: | 5702 |
| Genotype Strain: | 427 |
Factors:
Subject type: Cultured cells; Subject species: Trypanosoma brucei brucei (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA169163 | RBP42_KD_1 | Knockdown |
| SA169164 | RBP42_KD_4 | Knockdown |
| SA169165 | RBP42_KD_3 | Knockdown |
| SA169166 | RBP42_KD_2 | Knockdown |
| SA169167 | RBP42_WT_4 | Wild-type |
| SA169168 | RBP42_WT_1 | Wild-type |
| SA169169 | RBP42_WT_2 | Wild-type |
| SA169170 | RBP42_WT_3 | Wild-type |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO001892 |
| Collection Summary: | T. brucei Lister 427 bloodstream form RBP42 conditional knockdown cell line (RBP42Ty1) was grown in HMI-9 medium supplemented with 10% fetal bovine serum and 10% serum plus at 37C in a humidified incubator containing 5% CO2. Cultures were seeded at 1 x 10^5 cells/ml, passaged every 2-3 days and grown to a maximum of 1x10^6 cells per ml. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR001912 |
| Treatment Summary: | For metabolomic analysis, RBP42Ty1 cells were collected before and after two days of RBP42 depletion. Cells (2 x 10^7 cells/assay) were harvested and metabolites were extracted. |
Sample Preparation:
| Sampleprep ID: | SP001905 |
| Sampleprep Summary: | Metabolites were extracted with 1 ml of 40:40:20 mixture of methanol:acetonitrile:water plus 0.5% (V/V) formic acid on ice for 5 min. Following neutralization of formic acid by addition of 50 ul of 15% (m/V) NH4HCO3, cleared extracts were collected by centrifugation at 15000g for 10 min and stored at -80C. |
Combined analysis:
| Analysis ID | AN002958 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Plus Orbitrap |
| Ion Mode | NEGATIVE |
| Units | arbitrary |
Chromatography:
| Chromatography ID: | CH002191 |
| Chromatography Summary: | HILIC separation was performed on a Vanquish Horizon UHPLC system (Thermo Fisher Scientific, Waltham, MA) with an XBridge BEH Amide column (150 mm × 2.1 mm, 2.5 μm particle size, Waters, Milford, MA) using a gradient of solvent A (95%:5% H2O:acetonitrile with 20 mM acetic acid, 40 mM ammonium hydroxide, pH 9.4) and solvent B (20%:80% H2O:acetonitrile with 20 mM acetic acid, 40 mM ammonium hydroxide, pH 9.4). The gradient was 0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B; 16.5 min, 100% B; and 22 min, 100% B. The flow rate was 300 μl/min. The injection volume was 5 μL, and the column temperature was set to 25°C. The autosampler temperature was set to 4°C, and the injection volume was 5 µL. |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters Acquity BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 25 |
| Flow Gradient: | 0 min, 100% B; 3 min, 100% B; 3.2 min, 90% B; 6.2 min, 90% B; 6.5 min, 80% B; 10.5 min, 80% B; 10.7 min, 70% B; 13.5 min, 70% B; 13.7 min, 45% B; 16 min, 45% B; 16.5 min, 100% B; and 22 min, 100% B. |
| Flow Rate: | 300 µl/min |
| Solvent A: | 95% water/5% acetonitrile; 20 mM acetic acid; 40 mM ammonium hydroxide, pH 9.4 |
| Solvent B: | 20% water/80% acetonitrile; 20 mM acetic acid, 40 mM ammonium hydroxide, pH 9.4 |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS002748 |
| Analysis ID: | AN002958 |
| Instrument Name: | Thermo Q Exactive Plus Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Each sample was analyzed with a nominal resolution of 70,000. The automatic gain control target was 3×106. The maximum injection time was 50 ms. Scan range was 75-1,000. The targeted metabolite data analysis was performed in MAVEN. The compound identification was based on the accurate mass and the retention time learned from in-house chemical collection |
| Ion Mode: | NEGATIVE |
