Metabolomics Workbench : NIH Data Repository

MB Sample ID: SA078173

Local Sample ID:	PC3_CENPF_KO_004
Subject ID:	SU001194
Subject Type:	Cultured cells
Subject Species:	Homo sapiens
Taxonomy ID:	9606
Gender:	Not applicable

Select appropriate tab below to view additional metadata details:

Subject:

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

Factors:

Local Sample ID	MB Sample ID	Factor Level ID	Level Value	Factor Name
PC3_CENPF_KO_004	SA078173	FL011911	KO	CENPF

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 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 (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 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