Summary of Study ST003073

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001914. The data can be accessed directly via it's Project DOI: 10.21228/M89T5V This work is supported by NIH grant, U2C- DK119886.

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This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003073
Study TitleInvestigation of 3,5,3’-L-triiodothyronine (T3) and 3,5,3’5’-L-tetraiodothyronine (T4) by targeted LC-MS analysis from mouse adult or embryonic CSF and from adult serum.
Study SummaryTo maximize discovery from samples with limited amounts, we optimized a method to detect the thyroid hormones ( 3,5,3’-L-triiodothyronine (T3) and 3,5,3’5’-L-tetraiodothyronine (T4)) as well as polar metabolites from central carbon metabolism from mouse adult or embryonic CSF and from adult mouse serum. Samples were ran on reverse phase and HILIC chromatography respectively. For T3 and T4 analysis we utilized targeted analysis using information from previously ran synthetic standards. We interrogated relative changes between fresh and frozen adult (male or female) CSF compared to fresh and frozen embryonic CSF. This data presents the levels of T3 and T4 as interrogated by reverse phase chromatography
Institute
Boston Children's Hospital
DepartmentPathology
LaboratoryKanarek Lab
Last NamePetrova
First NameBoryana
Address300 Longwood Av
Emailboryana.petrova@childrens.harvard.edu
Phone6173557433
Submit Date2024-01-10
Num Groups7
Total Subjects19
Num Males8
Num Females6
Study Commentsembryos also investigated. samples split for fresh and frozen conditions
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2024-02-14
Release Version1
Boryana Petrova Boryana Petrova
https://dx.doi.org/10.21228/M89T5V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001914
Project DOI:doi: 10.21228/M89T5V
Project Title:Optimized Mass Spectrometry Detection of Thyroid Hormones and Polar Metabolites in Rodent Cerebrospinal Fluid
Project Summary:Thyroid hormones (TH) are required for brain development and function. Cerebrospinal fluid (CSF), which bathes the brain and spinal cord, contains TH as free hormone, or as bound to transthyretin (TTR). Tight TH level regulation in the central nervous system is essential for de-velopmental gene expression that governs neurogenesis, myelination, and synaptogenesis. This integrated function of TH highlights the importance of developing precise and reliable methods for assessing TH levels in CSF. We report an optimized liquid chromatography-mass spectrome-try (LC-MS) based method to measure TH in rodent CSF and serum, applicable to both fresh and frozen samples. Using this new method, we find distinct differences in CSF TH in pregnant dams vs. non-pregnant adults and in embryonic vs. adult CSF. Further, targeted LC-MS metabolic pro-filing uncovers distinct central carbon metabolism in the CSF of these populations. TH detection and metabolite profiling of related metabolic pathways open new avenues of rigorous research into CSF TH and will inform future studies on metabolic alterations in CSF during normal de-velopment.
Institute:Boston Children's Hospital
Department:Pathology
Laboratory:Kanarek Lab
Last Name:Petrova
First Name:Boryana
Address:300 Longwood Av
Email:boryana.petrova@childrens.harvard.edu
Phone:6173557433

Subject:

Subject ID:SU003188
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source Storage condition Sex
SA332284RF401Adult CSF Fresh Female
SA332285RF402Adult CSF Fresh Female
SA332286RF400Adult CSF Fresh Female
SA332287RF403Adult CSF Fresh Female
SA332288RF398Adult CSF Fresh Male
SA332289RF397Adult CSF Fresh Male
SA332290RF396Adult CSF Fresh Male
SA332291RF399Adult CSF Fresh Male
SA332292RF390Adult CSF Frozen Female
SA332293RF389Adult CSF Frozen Female
SA332294RF387Adult CSF Frozen Female
SA332295RF388Adult CSF Frozen Female
SA332296RF384Adult CSF Frozen Male
SA332297RF383Adult CSF Frozen Male
SA332298RF386Adult CSF Frozen Male
SA332299RF385Adult CSF Frozen Male
SA332300RF381Adult Mock Fresh Female
SA332301RF380Adult Mock Fresh Male
SA332302RF378Adult Mock Frozen Female
SA332303RF377Adult Mock Frozen Male
SA332304RF411Adult Serum Fresh Male
SA332305RF412Adult Serum Fresh Male
SA332306RF410Adult Serum Frozen Male
SA332307RF409Adult Serum Frozen Male
SA332308RF406Embryonic CSF Fresh -
SA332309RF405Embryonic CSF Fresh -
SA332310RF407Embryonic CSF Fresh -
SA332311RF408Embryonic CSF Fresh -
SA332312RF404Embryonic CSF Fresh -
SA332313RF395Embryonic CSF Frozen -
SA332314RF391Embryonic CSF Frozen -
SA332315RF394Embryonic CSF Frozen -
SA332316RF392Embryonic CSF Frozen -
SA332317RF393Embryonic CSF Frozen -
SA332318RF382Embryonic Mock Fresh -
SA332319RF379Embryonic Mock Frozen -
Showing results 1 to 36 of 36

Collection:

Collection ID:CO003181
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
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003197
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:SP003194
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 chloroform: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% ac-etonitrile (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.

Chromatography:

Chromatography ID:CH003802
Instrument Name:Thermo Vanquish
Column Name:Sigma Aldrich Ascentis Express C18 (150 × 2.1 mm, 2.7 um)
Column Temperature:30
Flow Gradient:The chromatographic gradient was run at a flow rate of 0.250 mL min−1 as follows: 0–2 min: held at 5% B; 2–12.1 min: linear gradient of 5% to 95% B; 12.1–17.0 min: 95% B; 17.1–21.0 min: gradient was returned to 5% B
Flow Rate:0.25 mL/min
Solvent A:100% water; 0.1% formic acid
Solvent B:100% acetonitrile; 0.1% formic acid.
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN005031
Analysis Type:MS
Chromatography ID:CH003802
Num Factors:14
Num Metabolites:2
Units:a.u.
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