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.

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	ST001133
Study Title	Downregulation of CENPF epigenetically remodels prostate cancer cells and alters cellular metabolism
Study 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
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
Submit Date	2019-01-14
Analysis Type Detail	GC-MS
Release Date	2020-01-06
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA078168	PC3_003	Control
SA078169	PC3_002	Control
SA078170	PC3_001	Control
SA078171	PC3_CENPF_KO_005	KO
SA078172	PC3_CENPF_KO_006	KO
SA078173	PC3_CENPF_KO_004	KO

Showing results 1 to 6 of 6

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.

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 (30m x 0.25mm,0.25um)
MS Type	EI
MS instrument type	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 (30m x 0.25mm,0.25um)
Chromatography Type:	GC

MS:

MS ID:	MS001718
Analysis ID:	AN001858
Instrument Name:	Leco Pegasus IV TOF
Instrument Type:	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