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MB Sample ID: SA211873
Local Sample ID: | 8020-S |
Subject ID: | SU002300 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 50-90 yrs |
Species Group: | Mammals |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002300 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Age Or Age Range: | 50-90 yrs |
Species Group: | Mammals |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
8020-S | SA211873 | FL025837 | Alzheimer patient | Condition |
8020-S | SA211873 | FL025837 | Shikonin | Treatment |
Collection:
Collection ID: | CO002293 |
Collection Summary: | For Metabolome, iNs were flow cytometry-isolated 21 days of conversion. iNs were sorted based on the expression of the PSA-NCAM surface markers using PSA-NCAM-PE (Miltenyi) and re-plated on Geltrex-coated wells. The following day, iNs were treated with 2.5 mM DGlucose-C13 for 6 hours and harvested using Tryple. Supernatant and cell pellets were shock frozen in liquid nitrogen. |
Sample Type: | Biopsy |
Treatment:
Treatment ID: | TR002312 |
Treatment Summary: | After two weeks of conversion, cells were treated for 10 days with shikonin (10 µM, ChemCruz) before FACS sorting. Control iNs were FACS-sorted and plated on Geltrex-coated wells before transduction with pLVXTP-EGFP-PKM2 or pLVXTP-EGFP. Around 60 % of all neurons were successfully transduced. Five days after transduction, iNs were harvested for MS-analysis. Alternatively, cells were treated with CoDo for 6 hours before harvest. |
Sample Preparation:
Sampleprep ID: | SP002306 |
Sampleprep Summary: | Metabolites from frozen cell pellets were extracted at 150,000 cells/mL in cold 5:3:2 MeOH:acetonitrile:water. Samples were vortexed 30 min at 4 degrees C then supernatants clarified by centrifugation (10 min, 10,000 g, 4 degrees C). Supernatants were split into two equal tubes and gently dried using a vacuum concentrator. One set of residues were resuspended in 12 uL of 0.1% formic acid (for positive ion mode). The other set of residues were resuspended in 12 uL of 1 mM ammonium acetate (for negative ion mode). |
Combined analysis:
Analysis ID | AN003622 | AN003623 |
---|---|---|
Analysis type | MS | MS |
Chromatography type | Reversed phase | Reversed phase |
Chromatography system | Thermo Vanquish | Thermo Vanquish |
Column | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
MS Type | ESI | ESI |
MS instrument type | Orbitrap | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
Ion Mode | NEGATIVE | POSITIVE |
Units | peak area | peak area |
Chromatography:
Chromatography ID: | CH002677 |
Chromatography Summary: | Negative C18 cells |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
Sample Injection: | 10 uL |
Chromatography Type: | Reversed phase |
Chromatography ID: | CH002678 |
Chromatography Summary: | Positive C18 cells |
Instrument Name: | Thermo Vanquish |
Column Name: | Phenomenex Kinetex C18 (150 x 2.1mm,1.7um) |
Sample Injection: | 10 uL |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS003373 |
Analysis ID: | AN003622 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
Ion Mode: | NEGATIVE |
MS ID: | MS003374 |
Analysis ID: | AN003623 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Resolution 70,000, scan range 65-900 m/z, maximum injection time 200 ms, microscans 2, automatic gain control (AGC) 3 x 10^6 ions, source voltage 4.0 kV, capillary temperature 320 C, and sheath gas 45, auxiliary gas 15, and sweep gas 0 (all nitrogen). Data converted to mzXML using RawConverter. Metabolites were annotated and integrated using Maven in conjunction with the KEGG database. |
Ion Mode: | POSITIVE |