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MB Sample ID: SA385752
| Local Sample ID: | HSA-000019576 |
| Subject ID: | SU003630 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 15 mo |
| Gender: | Male |
| Species Group: | Mammals |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003630 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Age Or Age Range: | 15 mo |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| HSA-000019576 | SA385752 | FL044530 | APP | genotype |
| HSA-000019576 | SA385752 | FL044530 | mid | condition |
| HSA-000019576 | SA385752 | FL044530 | mid_disease | group |
| HSA-000019576 | SA385752 | FL044530 | microglia | Sample source |
Collection:
| Collection ID: | CO003623 |
| Collection Summary: | Microglia isolation was performed using the Magnetic-activated cell sorting (MACS) system (Miltenyi Biotec). No CD11b enrichment step was performed as the intrinsic mKate2 reporter is only expressed in TREM2 expressing (microglia) cells. Hence, fluorescence-activated cell sorting was performed based on the mKate2 fluorescence signal and sorted into low, mid and high expressing subpopulations, as a proxy for the TREM2 expression of individual cells. |
| Sample Type: | microglia |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003639 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP003637 |
| Sampleprep Summary: | Pellets from the sorted subpopulations were reconstituted on ice in 9:1 MeOH:water including internal standards, vortexed for 1 minute, and spun down for 5 minutes at 10,000 g. Supernatant was transferred to glass vial for analysis by LC-MS. |
Combined analysis:
| Analysis ID | AN005746 | AN005747 | AN005748 | AN005749 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | HILIC | Ion exchange |
| Chromatography system | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II | Agilent 1290 Infinity II |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) | Imtakt Intrada Organic Acid (150 x 2mm, 3um) ) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Triple quadrupole | Triple quadrupole | Triple quadrupole | Triple quadrupole |
| MS instrument name | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap | ABI Sciex 6500+ Qtrap |
| Ion Mode | POSITIVE | POSITIVE | POSITIVE | NEGATIVE |
| Units | log2(area) | log2(area) | log2(area) | log2(area) |
Chromatography:
| Chromatography ID: | CH004361 |
| Chromatography Summary: | For each analysis, 5 µL of sample was injected on a BEH C18 1.7 µm, 2.1×100 mm column (Waters) using a flow rate of 0.25 mL/min at 55°C. For positive ionization mode, mobile phase A consisted of 60:40 acetonitrile/water (v/v) with 10 mM ammonium formate + 0.1% formic acid; mobile phase B consisted of 90:10 isopropyl alcohol/acetonitrile (v/v) with 10 mM ammonium formate + 0.1% formic acid. The gradient was programmed as follows: 0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 55 |
| Flow Gradient: | 0.0-8.0 min from 45% B to 99% B, 8.0-9.0 min at 99% B, 9.0-9.1 min to 45% B, and 9.1-10.0 min at 45% B. |
| Flow Rate: | 0.25 mL/min |
| Solvent A: | 60% acetonitrile/40% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 90% isopropyl alcohol/10% acetonitrile; 10 mM ammonium formate; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004362 |
| Chromatography Summary: | For each analysis, 5 µL of sample was injected on a BEH amide 1.7 µm, 2.1×150 mm column (Waters Corporation, Milford, Massachusetts, USA) using a flow rate of 0.40 mL/min at 40°C. Mobile phase A consisted of water with 10 mM ammonium formate + 0.1% formic acid. Mobile phase B consisted of acetonitrile with 0.1% formic acid. The gradient was programmed as follows: 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0.0–1.0 min at 95% B; 1.0–7.0 min to 50% B; 7.0–7.1 min to 95% B; and 7.1–10.0 min at 95% B |
| Flow Rate: | 0.40 mL/min |
| Solvent A: | 100% water; 10 mM ammonium formate; 0.1% formic acid |
| Solvent B: | 100% acetonitrile; 0.1% formic acid |
| Chromatography Type: | HILIC |
| Chromatography ID: | CH004363 |
| Chromatography Summary: | 5 µL of sample was injected on an Imtakt Intrada Organic Acid 3 µm, 2 x 150 mm (Imtakt USA, Portland, OR USA); using a flow rate of 0.2 mL/min at 60°C. For negative ionization mode, Mobile phase A consisted of acetonitrile/water/formic acid = 10/90/0.1%. Mobile phase B consisted of acetonitrile/ 100mM ammonium formate= 10/90%. The gradient was programmed as follows: 0.0–1.0 min at 0% B; 1.0–7.0 min to 100% B; 7.1 at 0% B; and 7.1-10 min at 0% B. |
| Instrument Name: | Agilent 1290 Infinity II |
| Column Name: | Imtakt Intrada Organic Acid (150 x 2mm, 3um) ) |
| Column Temperature: | 60 |
| Flow Gradient: | 0.0–1.0 min at 0% B; 1.0–7.0 min to 100% B; 7.1 at 0% B; and 7.1-10 min at 0% B. |
| Flow Rate: | 0.20 mL/min |
| Solvent A: | 10% acetonitrile/90% water; 0.1% formic acid |
| Solvent B: | 10% acetonitrile/90% water; 100mM ammonium formate |
| Chromatography Type: | Ion exchange |
MS:
| MS ID: | MS005469 |
| Analysis ID: | AN005746 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Curtain gas at 40 psi (positive mode); collision gas was set at medium; ion spray voltage at 5500 V (positive mode); temperature at 250°C (positive mode); ion source Gas 1 at 55 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V (positive mode); and collision cell exit potential at 12.5 V (positive mode). Quantification was performed using MultiQuant 3.02 (Sciex). |
| Ion Mode: | POSITIVE |
| MS ID: | MS005470 |
| Analysis ID: | AN005747 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Curtain gas at 40 psi (positive mode); collision gas was set at medium; ion spray voltage at 5500 V (positive mode); temperature at 250°C (positive mode); ion source Gas 1 at 55 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V (positive mode); and collision cell exit potential at 12.5 V (positive mode). Quantification was performed using MultiQuant 3.02 (Sciex). Increased MRM dwell time for specific list of TG transitions. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005471 |
| Analysis ID: | AN005748 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | curtain gas at 30 psi; collision gas was set at medium; ion spray voltage at 5500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at 60 psi; entrance potential at 10 V; and collision cell exit potential at 12.5 V. |
| Ion Mode: | POSITIVE |
| MS ID: | MS005472 |
| Analysis ID: | AN005749 |
| Instrument Name: | ABI Sciex 6500+ Qtrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | curtain gas at 40 V; collision gas was set at medium; ion spray voltage at -4500 V; temperature at 600°C; ion source Gas 1 at 50 psi; ion source Gas 2 at 60 psi; entrance potential at -10 V; and collision cell exit potential at -15.0 V. |
| Ion Mode: | NEGATIVE |
