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.

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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.
Institute
Arizona State University
DepartmentCollege of Health Solutions
Last NameLiu
First NameJingping
Address13208 E. Shea Blvd, Scottsdale, AZ
Emailjliu381@asu.edu
Phone4802078529
Submit Date2018-10-24
Raw Data File Type(s)d
Analysis Type DetailGC-MS
Release Date2018-12-11
Release Version1
Jingping Liu Jingping Liu
https://dx.doi.org/10.21228/M8ZM3X
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
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:

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
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