Summary of Study ST001086

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


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Study IDST001086
Study TitleTargeted GC-MS of SETD2 isogenic cell lines
Study SummaryIn 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.
Arizona State University
DepartmentCollege of Health Solutions
Last NameLiu
First NameJingping
Address13208 E. Shea Blvd, Scottsdale, AZ
Submit Date2018-10-24
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2018-12-11
Release Version1
Jingping Liu Jingping Liu application/zip

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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


Subject ID:SU001130
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606


Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA07342938-F rep1SETD2-mutation
SA07343038-F rep2SETD2-mutation
SA07343138-F rep3SETD2-mutation
SA07343238-E rep3SETD2-mutation
SA07343338-E rep2SETD2-mutation
SA07343438-E rep1SETD2-mutation
SA073435786-O rep2Wild-type
SA073436786-O rep3Wild-type
SA073437786-O rep1Wild-type
Showing results 1 to 9 of 9


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 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
Units pmole/ug


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 ID:MS001637
Analysis ID:AN001771
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
Ion Source Temperature:230°C
Ionization:70 eV
Scanning Range:50-600 m/z