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MB Sample ID: SA317984
Local Sample ID: | 26 |
Subject ID: | SU003041 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Select appropriate tab below to view additional metadata details:
Subject:
Subject ID: | SU003041 |
Subject Type: | Human |
Subject Species: | Homo sapiens |
Taxonomy ID: | 9606 |
Gender: | Male and female |
Factors:
Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
---|---|---|---|---|
26 | SA317984 | FL037850 | e3/e3 | APOE genotype |
26 | SA317984 | FL037850 | G/G | TMEM SNP |
Collection:
Collection ID: | CO003034 |
Collection Summary: | Homogenates were prepared by placing 10-20 mg of frozen tissue into 500 L of 20 mM Hepes pH 7.4, 10 mM KCl, EDTA-free cOmplete protease inhibitor cocktail (Roche), 1 mM dithiothreitol, and 3 mM β-glycerophosphate, and ultrasonicating for 5 min (30 s on/30 s off) at 4 °C in a Qsonica Q800R2 sonicating bath. Homogenates were cleared by centrifugation at 1000g for 10 min at 4 °C, and the supernatant was stored at -80 °C in 100 µL aliquots. Total protein concentrations were determined using the Bradford assay (Bio-Rad). Lipids were extracted from hippocampal homogenates (~100 µg protein) using a one phase butanol-methanol (BUME) (1:1 v/v) procedure [34]. The following internal standards were added to each sample: 5 nmoles of d19:0/19:0 PC, 2 nmoles of d18:1/17:0 SM, d18:1/12:0 HexCer, 17:0/17:0 PS, 17:0/17:0 PE, 17:0/17:0/17:0 TG, 17:0/17:0 PG, 14:0/14:0/14:0/14:0 cardiolipin, 17:0 cholesteryl ester, 1 nmole of 17:0/17:0 PA, d18:1/15:0-d7 PI, cholesterol-d7, 0.5 nmoles of d18:1/17:0 ST, d18:1/17:0 ceramide, 17:1 LPE, 17:1 LPS, 17:0 LPC, 18:1-d7 monoacylglycerol, d18:1/15:0-d7 diacylglycerol, d18:1/12:0 Hex2Cer, and 0.2 nmoles of 17:1 sphingosine, 17:1 sphingosine 1-phosphate, d3-16:0 acylcarnitine, 17:0 LPA. |
Sample Type: | Brain |
Treatment:
Treatment ID: | TR003050 |
Treatment Summary: | No treatment. This study investigated the effects of age, TMEM106B rs1990622 SNP, and APOE genotype on the lipidome of CA1 hippocampus from physiologically ageing individuals. |
Sample Preparation:
Sampleprep ID: | SP003047 |
Sampleprep Summary: | Lipids were extracted from hippocampal homogenates (~100 µg protein) using a one phase butanol-methanol (BUME) (1:1 v/v) procedure [34]. The following internal standards were added to each sample: 5 nmoles of d19:0/19:0 PC, 2 nmoles of d18:1/17:0 SM, d18:1/12:0 HexCer, 17:0/17:0 PS, 17:0/17:0 PE, 17:0/17:0/17:0 TG, 17:0/17:0 PG, 14:0/14:0/14:0/14:0 cardiolipin, 17:0 cholesteryl ester, 1 nmole of 17:0/17:0 PA, d18:1/15:0-d7 PI, cholesterol-d7, 0.5 nmoles of d18:1/17:0 ST, d18:1/17:0 ceramide, 17:1 LPE, 17:1 LPS, 17:0 LPC, 18:1-d7 monoacylglycerol, d18:1/15:0-d7 diacylglycerol, d18:1/12:0 Hex2Cer, and 0.2 nmoles of 17:1 sphingosine, 17:1 sphingosine 1-phosphate, d3-16:0 acylcarnitine, 17:0 LPA. |
Combined analysis:
Analysis ID | AN004802 |
---|---|
Analysis type | MS |
Chromatography type | Reversed phase |
Chromatography system | Thermo Vanquish |
Column | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) |
MS Type | ESI |
MS instrument type | Orbitrap |
MS instrument name | Thermo Q Exactive HF-X Orbitrap |
Ion Mode | UNSPECIFIED |
Units | % Total |
Chromatography:
Chromatography ID: | CH003630 |
Instrument Name: | Thermo Vanquish |
Column Name: | Waters ACQUITY UPLC BEH Amide (100 x 2.1mm,1.7um) |
Column Temperature: | 45 |
Flow Gradient: | Run time was 25 min using a binary gradient starting at 20% B for 3 min, increasing to 45% B from 3 - 5.5 min, then to 65% B from 5.5 - 8 min, then to 85% B from 8 - 13 min, then to 100% B from 13 - 14 min. The gradient was held at 100% B from 14 - 20 min, then decreased to 20% B and held to 25 min. |
Flow Rate: | 0.28 ml/min |
Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid |
Solvent B: | 10% acetonitrile/90% isopropanol; 10 mM ammonium formate; 0.1% formic acid |
Chromatography Type: | Reversed phase |
MS:
MS ID: | MS004548 |
Analysis ID: | AN004802 |
Instrument Name: | Thermo Q Exactive HF-X Orbitrap |
Instrument Type: | Orbitrap |
MS Type: | ESI |
MS Comments: | Each sample injected twice, once in positive and once in negative. |
Ion Mode: | UNSPECIFIED |