Summary of Study ST001909
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 PR001203. The data can be accessed directly via it's Project DOI: 10.21228/M86Q68 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 | ST001909 |
| Study Title | ATF3 regulation of serine metabolism |
| Study Type | stable isotope tracing |
| Study Summary | ATF3 is a common stress sensor, and its expression can be induced by serine deprivation. The goal of this project is to determine whether ATF3 regulates serine biosynthesis. ATF3-wildtype and –knockout cells are cultured in complete or serine-free medium supplemented with 13C-6-glucose for 24 h for stable isotope tracing. The results show that ATF3 appears to promote serine biosynthesis. |
| Institute | Augusta University |
| Last Name | Yan |
| First Name | Chunhong |
| Address | 1410 Laney Walker Blvd, Augusta, GA, 30912, USA |
| cyan@augusta.edu | |
| Phone | 7067210099 |
| Submit Date | 2021-08-11 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2021-10-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001203 |
| Project DOI: | doi: 10.21228/M86Q68 |
| Project Title: | ATF3 regulation of serine metabolism |
| Project Type: | Isotope Tracing, GC-MS |
| Project Summary: | ATF3 is a common stress sensor, and its expression can be induced by serine deprivation. The goal of this project is to determine whether ATF3 regulates serine biosynthesis. ATF3-wildtype and –knockout cells are cultured in complete or serine-free medium supplemented with 13C-6-glucose for 24 h for stable isotope tracing. The results show that ATF3 appears to promote serine biosynthesis. |
| Institute: | Augusta University |
| Department: | Georgia Cancer Center |
| Last Name: | Yan |
| First Name: | Chunhong |
| Address: | 1410 Laney Walker Blvd, Augusta, GA, 30912, USA |
| Email: | cyan@augusta.edu |
| Phone: | 7067210099 |
| Funding Source: | NIH/NCI R01CA240933, R01CA190429, R01CA236890 |
Subject:
| Subject ID: | SU001987 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Genotype Strain: | ATF3(+/+) vs ATF3(-/-) |
| Cell Strain Details: | HCT116 cells engineered to knockout ATF3 expression via rAAV-mediated homologous recombination |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype_Media supplement |
|---|---|---|
| SA176874 | Ding_C-3_015 | KO-complete |
| SA176875 | Ding_C-4_016 | KO-complete |
| SA176876 | Ding_C-6_018 | KO-complete |
| SA176877 | Ding_C-2_014 | KO-complete |
| SA176878 | Ding_C-5_017 | KO-complete |
| SA176879 | Ding_C-1_013 | KO-complete |
| SA176880 | Ding_D-2_020 | KO-serine(-) |
| SA176881 | Ding_D-1_019 | KO-serine(-) |
| SA176882 | Ding_D-3_021 | KO-serine(-) |
| SA176883 | Ding_D-4_022 | KO-serine(-) |
| SA176884 | Ding_D-5_023 | KO-serine(-) |
| SA176885 | Ding_D-6_024 | KO-serine(-) |
| SA176886 | Ding_A-3_003 | WT-complete |
| SA176887 | Ding_A-2_002 | WT-complete |
| SA176888 | Ding_A-4_004 | WT-complete |
| SA176889 | Ding_A-5_005 | WT-complete |
| SA176890 | Ding_A-6_006 | WT-complete |
| SA176891 | Ding_A-1_001 | WT-complete |
| SA176892 | Ding_B-4_010 | WT-serine(-) |
| SA176893 | Ding_B-3_009 | WT-serine(-) |
| SA176894 | Ding_B-5_011 | WT-serine(-) |
| SA176895 | Ding_B-6_012 | WT-serine(-) |
| SA176896 | Ding_B-2_008 | WT-serine(-) |
| SA176897 | Ding_B-1_007 | WT-serine(-) |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO001980 |
| Collection Summary: | Cells were counted, washed with cold PBS and then flash-frozen in liquid nitrogen |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR001999 |
| Treatment Summary: | HCT116 cells (~50% confluence) were washed with PBS, and cultured in HEPES buffered Krebs-Ringer solution supplemented with 25 mM [U-13C]-D-glucose, 10% dialysed FBS, 2×MEM amino acids, 2× Vitamin Solution and 4 mM L-glutamine, with or without 0.4 mM serine and glycine, for 24 h. Cells were washed with PBS and metabolites extracted using 1 mL of acetonitrile:isopropanol:water (3:3:2, v/v/v) mixture. |
Sample Preparation:
| Sampleprep ID: | SP001993 |
| Sampleprep Summary: | The extraction solvent was degassed and pre-chilled at −20°C. Samples were homogenized using Geno/Grinder 2010 (SPEX SamplePrep) at 1500 rpm for 30s, then shaken at 4°C for 5 min and centrifuged for 2 minutes at 14,000 rcf. 450 μL supernatant was transferred to a new tube and dried down using Centrivap cold trap concentrator (Labconco). 10 μL of methoxyamine hydrochloride in pyridine (40 mg/mL) was added to dried sample and shaken at 30°C for 1.5 hours for methoximation. 90 μL of N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA, Sigma-Aldrich) was used for tertbutylsilylation. C8–C30 fatty acid methyl esters (FAMEs) were added to MTBSTFA as internal standards for retention time correction. Samples were shaken at 37°C for 30 min for TMS or shaken at 80°C for 30 min for TBS and then ready for injection. |
Combined analysis:
| Analysis ID | AN003106 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| MS Type | EI |
| MS instrument type | GC-TOF |
| MS instrument name | Agilent 7890A |
| Ion Mode | UNSPECIFIED |
| Units | enrichment percentage |
Chromatography:
| Chromatography ID: | CH002293 |
| Chromatography Summary: | Gas chromatography-Quadrupole-time of flight mass spectrometry (GC-Q-TOF MS) was used for Stable Isotope enrichment. Rtx-5Sil MS column (30m length, 0.25 mm i.d, 0.25 μM 95% dimethyl 5% diphenyl polysiloxane film) with an additional 10 m guard column was installed on Agilent 7890 GC (Agilent Technologies). 99.9999% pure Helium gas was used as a mobile phase with a flow rate of 1mL/min. GC temperature was held at 50°C for 1 min, ramped at 20°C/min to 330°C and then held for 5 min. Electron ionization at -70eV was employed on a Agilent 7250 Quadrupole time of flight mass spectrometer (Agilent Technologies) with ion source temperature at 250°C and detector voltage at 1850V. Mass spectra were acquired at an acquisition rate of 5 spectra/s, with a scan range of 85-900 Da. |
| Instrument Name: | Agilent 7890A |
| Column Name: | Restek Rtx-5Sil (30m x 0.25mm,0.25um) |
| Chromatography Type: | GC |
MS:
| MS ID: | MS002888 |
| Analysis ID: | AN003106 |
| Instrument Name: | Agilent 7890A |
| Instrument Type: | GC-TOF |
| MS Type: | EI |
| MS Comments: | Agilent MassHunter Quantitative Analysis software B.10.00 (Agilent Technologies) was used for post data processing. |
| Ion Mode: | UNSPECIFIED |
