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MB Sample ID: SA078170
Local Sample ID: | PC3_001 |
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_001 | SA078170 | FL011910 | Control | 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 30C. 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 |