Summary of study ST001133

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 PR000758. The data can be accessed directly via it's Project DOI: 10.21228/M8Q10R This work is supported by NIH grant, U2C- DK119886.

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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.

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Study IDST001133
Study TitleDownregulation of CENPF epigenetically remodels prostate cancer cells and alters cellular metabolism
Study SummaryThis study aimed to determine the metabolic profile of CENPF-knockout (CENPFKO) PC cells and identify differentially expressed metabolites (DEMs) that can be used as diagnostic markers.
Institute
Cedars-Sinai Medical Center
Last NameKim
First NameJayoung
Address8700 Beverly Blvd., Davis 5071 Los Angeles, CA 90048, USA
EmailJayoung.Kim@cshs.org
Phone310-423-7168
Submit Date2019-01-14
Analysis Type DetailGC-MS
Release Date2020-01-06
Release Version1
Jayoung Kim Jayoung Kim
https://dx.doi.org/10.21228/M8Q10R
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000758
Project DOI:doi: 10.21228/M8Q10R
Project Title:Downregulation of CENPF epigenetically remodels prostate cancer cells and alters cellular metabolism
Project Summary:This study aimed to determine the metabolic profile of CENPF-knockout (CENPFKO) PC cells and identify differentially expressed metabolites (DEMs) that can be used as diagnostic markers.
Institute:Cedars-Sinai Medical Center
Department:Departments of Surgery and Biomedical Sciences
Last Name:Kim
First Name:Jayoung
Address:8700 Beverly Blvd., Davis 5071 Los Angeles, CA 90048, USA
Email:Jayoung.Kim@cshs.org
Phone:310-423-7168

Subject:

Subject ID:SU001194
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Not applicable

Factors:

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

mb_sample_id local_sample_id CENPF
SA078168PC3_003Control
SA078169PC3_002Control
SA078170PC3_001Control
SA078171PC3_CENPF_KO_005KO
SA078172PC3_CENPF_KO_006KO
SA078173PC3_CENPF_KO_004KO
Showing results 1 to 6 of 6

Collection:

Collection ID:CO001188
Collection Summary:Human PC3 cells were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA).
Sample Type:Prostate

Treatment:

Treatment ID:TR001209
Treatment Summary:CENPFKO PC3 cell line was constructed using the CRISPR/Cas9 system by ALSTEM, LLC (Richmond, CA).

Sample Preparation:

Sampleprep ID:SP001202
Sampleprep Summary:Samples were dissolved in 1 ml -20'C mixture of acetonitrile, isopropanol, and water (3:3:2 v/v) at a pH of 7. The solution was then vortexed at 4'C for 5 min. Samples were centrifuged for 2 min at 14,000 rcf and 500 ul were aliquoted. The aliquots were then evaporated in a Labconco Centrivap Cold Trap to complete dryness. The methoximation step was performed using a 10 ul solution of 40 mg/ml O-methylhydroxylamine hydrochloride (CAS: [593-56-6]; Formula: CH5NO.HCl) and shaken for 90 min at 30C. Then, 90 ul of N-methyl-N-trimethylsilyltrifluoroacetamide (MSTFA) was added and the solution was shaken for 30 min at 37'C. After, a 1 ul mixture of fatty acid methyl ester (FAME) retention time markers were added. The mixture was transferred to amber crimp autosampler vials.

Combined analysis:

Analysis ID AN001858
Analysis type MS
Chromatography type GC
Chromatography system Agilent 6890N
Column Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
MS Type EI
MS instrument type GC x GC-TOF
MS instrument name Leco Pegasus IV TOF
Ion Mode POSITIVE
Units normalized intensity

Chromatography:

Chromatography ID:CH001345
Chromatography Summary:An Agilent 6890GC with an Agilent 6890 Split/Splitless Injector was used. The column used was a Restek RTX-5Sil MS (95% dimethyl/5% diphenyl polysiloxane) with a 30 m length, 0.25 mm i.d., 0.25 um film thickness, and an additional 10 m guard column.
Instrument Name:Agilent 6890N
Column Name:Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
Chromatography Type:GC

MS:

MS ID:MS001718
Analysis ID:AN001858
Instrument Name:Leco Pegasus IV TOF
Instrument Type:GC x GC-TOF
MS Type:EI
MS Comments:Detection or deconvolution of peaks and compounds was performed using the Leco ChromaTOF software. Spectra were matched against the FiehnLib Mass Spectral and Retention Index Library.Post-curation and peak replacements were done using the in-house developed BinBase software, which was set as follows: validity of chromatogram (<10 peaks with intensities >107 counts/sec), unbiased retention index marker detection (MS similarity >800, validity of intensity range for high m/z marker ions), and retention index calculation by 5th order polynomial regression.
Ion Mode:POSITIVE
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