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MB Sample ID: SA252367
Local Sample ID: | Natural_abundance1 |
Subject ID: | SU002606 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU002606 |
Subject Type: | Mammal |
Subject Species: | Mus musculus |
Taxonomy ID: | 10090 |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
Natural_abundance1 | SA252367 | FL032078 | Wild-type | Genotype |
Natural_abundance1 | SA252367 | FL032078 | Control | Treatment |
Collection:
Collection ID: | CO002599 |
Collection Summary: | Collect embryonic stem cell derived eye organoids without isotopic labeling. Three biologically independent repeated samples were collected. |
Collection Protocol Filename: | Glucose_and_lactate_isotope_labeling.pdf |
Sample Type: | Retina |
Treatment:
Treatment ID: | TR002618 |
Treatment Summary: | No treatment was perfomed. |
Sample Preparation:
Sampleprep ID: | SP002612 |
Sampleprep Summary: | The eye organoids were collected and washed twice with PBS before pellets were flash-frozen and stored at −80°C until metabolite extraction. Metabolite analysis was performed as described previously (PMID: 33931446). Briefly, for metabolite extraction, 80% methanol was used followed by the rapid freeze-thaw method to break the tissues. The supernatant underwent speedvac drying. The samples were prepared in 80% acetonitrile and were analyzed by High-Resolution Liquid Chromatography Tandem Mass Spectrometry (LC-MS/MS). |
Combined analysis:
Analysis ID | AN004128 |
---|---|
Analysis type | MS |
Chromatography type | HILIC |
Chromatography system | Q-exactive |
Column | Waters XBridge BEH Amide (100 x 3.0mm, 3.5um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive Orbitrap |
Ion Mode | UNSPECIFIED |
Units | Peak area |
Chromatography:
Chromatography ID: | CH003058 |
Instrument Name: | Q-exactive |
Column Name: | Waters XBridge BEH Amide (100 x 3.0mm, 3.5um) |
Column Temperature: | 40 |
Flow Gradient: | 0 min, 15% A; 2.5 min, 30% A; 7 min, 43% A; 16 min, 62% A; 16.1-18 min, 75% A; 18-25 min, 15% A with a flow rate of 150 μL/min |
Flow Rate: | 150 μL/mi |
Solvent A: | 95% water/5% acetonitrile; 10 mM ammonium hydroxide; 10 mM ammonium acetate, pH 9.0 |
Solvent B: | 100% acetonitrile |
Chromatography Type: | HILIC |
MS:
MS ID: | MS003875 |
Analysis ID: | AN004128 |
Instrument Name: | Thermo Q Exactive Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | The capillary of the ESI source was set to 275 °C, with sheath gas at 35 arbitrary units, auxiliary gas at 5 arbitrary units and the spray voltage at 4.0 kV. In positive/negative polarity switching mode, an m/z scan range from 60 to 900 was chosen and MS1 data was collected at a resolution of 70,000. The automatic gain control (AGC) target was set at 1 × 106 and the maximum injection time was 200 ms. The top 5 precursor ions were subsequently fragmented, in a data-dependent manner, using the higher energy collisional dissociation (HCD) cell set to 30% normalized collision energy in MS2 at a resolution power of 17,500. Besides matching m/z, metabolites are identified by matching either retention time with analytical standards and/or MS2 fragmentation pattern. Data acquisition and analysis were carried out by Xcalibur 4.1 software and Tracefinder 4.1 software, respectively (both from Thermo Fisher Scientific) |
Ion Mode: | UNSPECIFIED |