Summary of Study ST001086
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 PR000725. The data can be accessed directly via it's Project DOI: 10.21228/M8ZM3X This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST001086 |
| Study Title | Targeted GC-MS of SETD2 isogenic cell lines |
| Study Summary | In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and the cellular metabolic changes of 786-O (WT) and 38E/38F isogenic cell lines (n=3 per group) were analyzed by GC-MS-based targeted metabolomics. |
| Institute | Arizona State University |
| Department | College of Health Solutions |
| Last Name | Liu |
| First Name | Jingping |
| Address | 13208 E. Shea Blvd, Scottsdale, AZ |
| jliu381@asu.edu | |
| Phone | 4802078529 |
| Submit Date | 2018-10-24 |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS |
| Release Date | 2018-12-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000725 |
| Project DOI: | doi: 10.21228/M8ZM3X |
| Project Title: | Targeted metabolomics of SETD2 isogenic cell lines |
| Project Summary: | SETD2, the histone methyltransferase responsible for the trimethylation of H3K36, is inactivated in approximately 10-32% of clear renal cell carcinoma (ccRCC) cases. To reveal the impact of SETD2 loss on metabolic alterations in ccRCC. In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and the cellular metabolic changes were analyzed by GC-MS-based targeted metabolomics. |
| Institute: | Arizona State University |
| Department: | College of Health Solutions |
| Last Name: | Liu |
| First Name: | Jingping |
| Address: | 13208 E. Shea Blvd, Scottsdale, AZ |
| Email: | jliu381@asu.edu |
| Phone: | 4802078529 |
Subject:
| Subject ID: | SU001130 |
| Subject Type: | Cultured cells |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
Factors:
Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA073429 | 38-F rep1 | SETD2-mutation |
| SA073430 | 38-F rep2 | SETD2-mutation |
| SA073431 | 38-F rep3 | SETD2-mutation |
| SA073432 | 38-E rep3 | SETD2-mutation |
| SA073433 | 38-E rep2 | SETD2-mutation |
| SA073434 | 38-E rep1 | SETD2-mutation |
| SA073435 | 786-O rep2 | Wild-type |
| SA073436 | 786-O rep3 | Wild-type |
| SA073437 | 786-O rep1 | Wild-type |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO001124 |
| Collection Summary: | Quickly aspirate cell culture medium from 3.5 cm plates, gently dispense 2 mL of PBS to rinse cells, shake the plate back and forth for 2 s and then quickly remove the PBS. Immediately add 1 mL 8:2 methanol:H2O (on dry ice) into the plates placed on dry ice to quench cell metabolism, store samples at -80℃. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR001144 |
| Treatment Summary: | The cell lines including 786-O and 38E/38F were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 2 mM L-glutamine. After culture at 37 °C, 5% CO2 condition for 24 h, the cells were collected for GC-MS analysis. |
Sample Preparation:
| Sampleprep ID: | SP001137 |
| Sampleprep Summary: | Sampleprep Summary: Scrape all the cells from culture dishes on dry ice, and transfer them into a 2 mL Eppendorf, spin the mixture at 14000 rpm for 10 min at 4°C. Remove all the soluble extract into a vial and completely dry samples. The extracted samples were incubated with 30 μL O-methylhydroxylamine hydrochloride solution in pyridine (Sigma-Aldrich, St. Louis, MO, USA) at 60°C for 90 min. Next, 70 μL of N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) were added and placed at 60 °C for 30 min. After centrifuge at 14000 rpm for 10 min, 70 μL of supernatant was transferred to a clean glass GC insert tube. |
Combined analysis:
| Analysis ID | AN001771 |
|---|---|
| Analysis type | MS |
| Chromatography type | GC |
| Chromatography system | Agilent 7890A |
| Column | Agilent DB5-MS (30m × 0.25mm, 0.25um) |
| MS Type | EI |
| MS instrument type | Single quadrupole |
| MS instrument name | Agilent 5975C |
| Ion Mode | POSITIVE |
| Units | pmole/ug |
Chromatography:
| Chromatography ID: | CH001251 |
| Instrument Name: | Agilent 7890A |
| Column Name: | Agilent DB5-MS (30m × 0.25mm, 0.25um) |
| Flow Rate: | 0.5 mL/min |
| Injection Temperature: | 250°C |
| Transferline Temperature: | 290°C |
| Chromatography Type: | GC |
MS:
| MS ID: | MS001637 |
| Analysis ID: | AN001771 |
| Instrument Name: | Agilent 5975C |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| Ion Mode: | POSITIVE |
| Ion Source Temperature: | 230°C |
| Ionization: | 70 eV |
| Scanning Range: | 50-600 m/z |
