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MB Sample ID: SA244208
| Local Sample ID: | SC_20201109_HILICp_FMS_CSF_F06_C_1_1 |
| Subject ID: | SU002531 |
| 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: | SU002531 |
| 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 |
|---|---|---|---|---|
| SC_20201109_HILICp_FMS_CSF_F06_C_1_1 | SA244208 | FL030616 | CONTROL | Genotype |
| SC_20201109_HILICp_FMS_CSF_F06_C_1_1 | SA244208 | FL030616 | m | sex |
| SC_20201109_HILICp_FMS_CSF_F06_C_1_1 | SA244208 | FL030616 | 51 | age |
Collection:
| Collection ID: | CO002524 |
| Collection Summary: | CSF samples were collected from 60 participants as part of the CHDI HD-Clarity study. There were 16 PRE, 16 MAN, 16 LATE HD participants and 12 control participants. Disease stage was determined using the diagnostic confidence level (DCL), length of CAG expansion and burden of pathology calculated from (CAG expansion – 35.5) x Age. Control participants were individuals without a known history of Huntington Disease (HD). All HD participants have a CAG expansion of > 40. PRE participants were not motor manifest as indicated by a DCL of <4 and a burden of pathology of > 250. MAN participants had a DCL =4 and a total functional capacity (TFC) between 7-13. The LATE group had all the above criteria for MAN and a TFC score between 0-6. Repeat CSF and blood samples collected 4-8 weeks after a baseline (BL) visit are provided for all control and PRE participants. Participants’ age and gender are reported here. Three participants (2 PRE, 1 MAN) were taking supplemental vitamins; however, their metal levels were similar to those in their corresponding participant group and thus, the data from these participants are included. Basic demographics like age and gender were reported previously in addition to participants' scores on a battery of cognitive, behavioral and motor assessments including the symbol digit modality test (SDMT), Stroop Word Reading (SWR), total functional capacity (TFC), total motor score (TMS) and the recently developed cUHDRS. |
| Collection Protocol Filename: | Sample_Collection.pdf |
| Sample Type: | CSF |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002543 |
| Treatment Summary: | No treatment |
Sample Preparation:
| Sampleprep ID: | SP002537 |
| Sampleprep Summary: | CSF samples collected were flash frozen and stored at -80°C until analyzed via Liquid ChromatographyHigh Resolution Mass Spectrometry (LC-HRMS and LC-HRMS/MS)-based metabolomics in the Vanderbilt Center for Innovative Technology (CIT) using previously described methods (cite). Briefly, equal volumes (100 µL) of previously frozen CSF was diluted with 100 µL ice-cold lysis buffer (1:1:2, Acetonitrile:MeOH:Ammonium Bicarbonate 0.1M, pH 8.0, LC-MS grade). Addition of isotopically labeled phenylalanine-D8 and biotin-D2 were added to individual samples prior to protein precipitation by addition of 800 µL of ice-cold methanol. Following overnight incubation at -80°C, precipitated proteins were pelleted by centrifugation at 10,000 rpm for 10 min and metabolite extracts were dried down in vacuo and stored at -80°C until reconstitution prior to MS analysis. |
Combined analysis:
| Analysis ID | AN003979 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Vanquish |
| Column | Waters ACQUITY UPLC BEH HILIC (100 x 2.1mm,1.7um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive HF hybrid Orbitrap |
| Ion Mode | POSITIVE |
| Units | time_m/z |
Chromatography:
| Chromatography ID: | CH002942 |
| Chromatography Summary: | CSF extracts (5uL injection volume) were separated on an ACQUITY UPLC BEH Amide HILIC 1.7μm, 2.1 × 100 mm column (Waters Corporation, Milford, MA) held at 30°C as previously described (cite). Briefly, liquid chromatography was performed at 200 µL min−1 using solvent A (5 mM ammonium formate in 90% water, 10% acetonitrile and 0.1% formic acid) and solvent B (5 mM ammonium formate in 90% acetonitrile, 10% water and 0.1% formic acid) with a gradient length of 30 min. |
| Methods Filename: | Metabolomics_Analyses.pdf |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Waters ACQUITY UPLC BEH HILIC (100 x 2.1mm,1.7um) |
| Column Temperature: | 30 |
| Flow Gradient: | 30 min |
| Flow Rate: | 0.20mL/min |
| Solvent A: | 90% water, 10% acetonitrile, 5mM Ammonium Formate, 0.1%FA |
| Solvent B: | 10% water, 90% acetonitrile, 5mM Ammonium Formate, 0.1%FA |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003713 |
| Analysis ID: | AN003979 |
| Instrument Name: | Thermo Q Exactive HF hybrid Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Full MS analyses were acquired over the mass-to-charge ratio (m/z) range of 70-1,050 in positive ion mode. Full mass scan was acquired at 120,000 resolution with a scan rate of 3.5 Hz, automatic gain control (AGC) target of 1x106, and maximum ion injection time of 100 ms, and MS/MS spectra were collected at 15,000 resolution, AGC target of 2x105 ions, with a maximum ion injection time of 100 ms |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | Metabolomics_Analyses.pdf |
