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MB Sample ID: SA332250

Local Sample ID:RF401
Subject ID:SU003187
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

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Subject:

Subject ID:SU003187
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

Local Sample IDMB Sample IDFactor Level IDLevel ValueFactor Name
RF401SA332250FL039316Adult CSFSample type
RF401SA332250FL039316FreshStorage condition
RF401SA332250FL039316FemaleSex

Collection:

Collection ID:CO003180
Collection Summary:Animals The Boston Children’s Hospital IACUC approved all experiments involving mice in this study. Adult CD-1 male and female mice and pregnant CD-1 dams were obtained from Charles River Laboratories. Sprague Dawley rats were purchased from Charles River Laboratories. Animals were housed in a temperature- and humidity-controlled room (70 ± 3 °F, 35–70% humidity) on a 12 h light/12 h dark cycle (7 a.m. on 7 p.m. off) and had free access to food and water. All animals younger than postnatal day 10 were al-located into groups based solely on the gestational age without respect to sex (both males and females were included). For studies involving rodents older than 10 days, sex was treated as a variable. Serum and CSF collection CSF was collected from the cisterna magna of adult (≥ 3 months old) or embryonic (E14.5) wild-type CD-1 mice. Independent samples (n) were defined as independent animals for adult samples, and as a CSF pool from all embryos in a single litter for embryonic CSF samples. Samples were maintained on ice, then spun 1000 × g for 10 min at 4 °C. The supernatant was collected and used for analysis. Blood was collected from cardiac puncture, allowed to clot for 10 minutes at room temperature, spun at 500 × g for 10 min at room temperature. The supernatant serum was collected and used for analysis.
Sample Type:Cerebrospinal fluid

Treatment:

Treatment ID:TR003196
Treatment Summary:No treatments were performed. All animals were CD-1 wild type. We compared different groups based on samples storage condition (fresh, frozen, or 24h stored), animal sex (female or male), or type of biofluid (serum, adult CSF, and embryonic CSF)

Sample Preparation:

Sampleprep ID:SP003193
Sampleprep Summary:Sample preparation for LC-MS analysis of thyroid hormone metabolites from CSF and serum in parallel to analysis for polar metabolites. Per condition, 5–10 μL of CSF or serum was extracted in 4:6:3 chloro-form:methanol:water mixture supplemented with isotopically labeled T3 and T4 (at 100 nM, Cambridge Isotope Laboratories, CLM-7185-C and CLM-8931-PK) and isotopically labeled 17 amino acids (at 1/5000, Cambridge Isotope Laboratories, MSK-A2-1.2) and isotopically labeled reduced glutathione (at 1 µM, Cambridge Isotope Laboratories and CNLM-6245-10). After centrifugation for 10 min at maximum speed on a benchtop centrifuge (Eppendorf) the top, hydrophilic layer was transferred to a new tube, dried using a nitrogen dryer (ThermoFisher Scientific, TS-18826) and reconstituted in 20 µL 70% acetonitrile (supplemented with QReSS, Cambridge Isotope Laboratories, MSK-QRESS-KIT) by brief vortexing. Extracted metabolites were spun again and cleared supernatant was transferred to LC-MS micro vials. The protocol was used for both fresh and frozen CSF and serum samples. A small amount of each sample was also pooled and serially diluted 3- and 10-fold to be used as quality controls throughout the run of each batch. Serum and CSF sample pools were kept separate and serum and CSF sample sets were run consecutively on our chromatography to avoid interspersing the run of two different matrixes.
Processing Storage Conditions:On ice
Extract Storage:-80℃

Combined analysis:

Analysis ID AN005030
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column SeQuant ZIC- pHILIC (150 x 2.1mm,5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units a.u.

Chromatography:

Chromatography ID:CH003801
Chromatography Summary:Analysis of polar metabolites by HILIC chromatography
Instrument Name:Thermo Vanquish
Column Name:SeQuant ZIC- pHILIC (150 x 2.1mm,5um)
Column Temperature:25
Flow Gradient:0–20 min: 0–20 min: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B at 150 mL/min flow rate.
Flow Rate:0.25 mL/min
Solvent A:100% acetonitrile
Solvent B:100% water; 20 mM ammonium carbonate, 0.1% ammonium hydroxide
Chromatography Type:HILIC

MS:

MS ID:MS004769
Analysis ID:AN005030
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:MS Data Acquisition Conditions for Targeted Analysis of Polar Metabolites and Thyroid Hormones: MS data acquisition was performed using a Q Exactive Orbitrap benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher Scientific, San Jose, CA, USA) in positive and negative ionization mode in a range of m/z = 70–1000, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 20 msec. A narrower scan in positive mode at m/z = 600–800 was used for more specific detection of TH. The resolution was set at 70,000, the AGC target was 5 × 105, and the max IT was 100 msec. For polar metabolites, HESI conditions were as follows: sheath gas flow rate: 35 units; Aug gas flow rate: 8 units; sweet gas flow rate: 1 unit; spray voltage: 3.5 kV (pos), 2.8 kV (neg); capillary temperature: 320 °C; S-lens RF: 50; Aux gas heater temperature: 350 °C. For T3/T4, HESI conditions were as follows: sheath gas flow rate: 40 units; Aug gas flow rate: 10 units; sweet gas flow rate: 0; spray voltage: 3.5 kV (pos), 2.8 kV (neg); capillary temperature: 380 °C; S-lens RF: 60; Aux gas heater temperature: 420 °C. Targeted Metabolomics Data Analysis: Relative quantification of polar metabolites was performed with TraceFinder 5.1 (Thermo Fisher Scientific, Waltham, MA, USA) using a 5 ppm mass tolerance and referencing an in-house library of chemical standards (see associated Supplemental Dataset S1). We routinely queried 266 compounds (40 internal standards and 226 metabolites). Pooled samples and fractional dilutions were prepared as quality controls and injected at the beginning and end of each run. In addition, pooled samples were interspersed throughout the run to control for technical drift in signal quality as well as to serve to assess the coefficient of variability (CV) for each metabolite. Data from TraceFinder were further consolidated and normalized with an in-house R script, freely accessible at github (https://github.com/FrozenGas/KanarekLabTraceFinderRScripts/blob/main/MS_data_script_v2.4_20221018.R). Briefly, this script performs the following normalization and quality control steps: (1) extracts and combines the peak areas from TraceFinder output.csvs; (2) calculates and normalizes to an averaged factor from all mean-centered chromatographic peak areas of isotopically labeled amino acid and QReSS internal standards within each sample; (3) filters out low-quality metabolites based on user-inputted cut-offs calculated from pool reinjections and pool dilutions; (4) calculates and normalizes for biological material amounts based on the total integrated peak area values of high-confidence metabolites. In this study, the linear correlation between the dilution factor and the peak area cut-offs is set to RSQ > 0.95 and the coefficient of variation (CV) < 30%. Finally, data were log transformed and Pareto scaled within the MetaboAnalyst-based statistical analysis platform [42] to generate PCA, PLSDA, volcano plots, and heatmaps. Individual metabolite bar plots and statistics were calculated in Excel (v16.81) and GraphPad Prism (v.10).
Ion Mode:UNSPECIFIED
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