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MB Sample ID: SA317924

Local Sample ID:21
Subject ID:SU003041
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

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Subject:

Subject ID:SU003041
Subject Type:Human
Subject Species:Homo sapiens
Taxonomy ID:9606
Gender:Male and female

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
21SA317924FL037841e2/e2APOE genotype
21SA317924FL037841A/GTMEM 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 1000g 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
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