Summary of Study ST002707

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR001678. The data can be accessed directly via it's Project DOI: 10.21228/M8T146 This work is supported by NIH grant, U2C- DK119886.


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 IDST002707
Study TitleLevels of T3 (triiodothyronine) and T4 (thyroxine) in CSF (cerebrospinal fluid) and plasma as part of natural diurnal variation
Study SummaryThis study employs targeted LC-MS analysis of CSF and plasma to assess relative changes in the levels of thyroid hormone (T3: triiodothyronine and T4: thyroxine) at two time points in the diurnal cycle. For this purpose, wild-type CD1 mice were kept in a circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off) and tissues were collected consistently at an a.m and a p.m time point (9 a.m. and 9 p.m). CSF was collected from adult (3 months old). Internal standards (13C-labelled T3 and T4) as well as calibration curves were used to estimate the respective T3 and T4 concentration in the examined biofluids.
Boston Children's Hospital, Harvard Medical School
LaboratoryKanarek Lab
Last NamePetrova
First NameBoryana
AddressEnders 1116.2 300 Longwood Ave
Submit Date2023-05-15
Num Groups2
Total Subjects27
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-05-28
Release Version1
Boryana Petrova Boryana Petrova application/zip

Select appropriate tab below to view additional metadata details:


Project ID:PR001678
Project DOI:doi: 10.21228/M8T146
Project Title:Combining multi-omics and real-time optics to track diurnal transitions in the choroid plexus and CSF at molecular, spatial, and temporal resolution
Project Summary:The choroid plexus (ChP) comprises the blood-CSF barrier and regulates cerebrospinal fluid (CSF) composition. Details of ChP-CSF regulation throughout the day remain unknown, largely due to lack of tools. We developed a platform for analyzing diurnal variations in mouse ChP function. We demonstrate widespread diurnal regulation of ChP secretion and barrier function across hours during the circadian day and in response to feeding cues, resulting in changes in CSF composition. ChP metabolomics uncovered increased dark phase oxidation. Transthyretin (TTR), a thyroid hormone chaperone, exhibited strong diurnal regulation and CSF-TTR levels varied across the day in register with CSF thyroid hormone levels and ChP-TTR expression. Our data will serve as a resource for the community, enabling better understanding of circadian rhythms and ChP diurnal function and regulation.
Institute:Boston Childrens Hospital
Laboratory:Kanarek Lab
Last Name:Petrova
First Name:Boryana
Address:300 Longwood Av, Boston, MA, 2115, USA
Contributors:Boryana Petrova, Ryann Fame


Subject ID:SU002812
Subject Type:Mammal
Subject Species:Mus musculus


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

mb_sample_id local_sample_id Diurnal_Cycle
SA272184RF176B0.2nM T3 standard
SA272185RF1760.2nM T3 standard
SA272186RF1830.2nM T4 standard
SA272187RF183B0.2nM T4 standard
SA272188RF1750nM T3 standard
SA272189RF175B0nM T3 standard
SA272190RF1820nM T4 standard
SA272191RF182B0nM T4 standard
SA272192RF179B200nM T3 standard
SA272193RF179200nM T3 standard
SA272194RF186200nM T4 standard
SA272195RF186B200nM T4 standard
SA272196RF17820nM T3 standard
SA272197RF178B20nM T3 standard
SA272198RF185B20nM T4 standard
SA272199RF18520nM T4 standard
SA272200RF181B20uM T3 standard
SA272201RF18120uM T3 standard
SA272202RF188B20uM T4 standard
SA272203RF18820uM T4 standard
SA272204RF177B2nM T3 standard
SA272205RF1772nM T3 standard
SA272206RF1842nM T4 standard
SA272207RF184B2nM T4 standard
SA272208RF1802uM T3 standard
SA272209RF180B2uM T3 standard
SA272210RF187B2uM T4 standard
SA272211RF1872uM T4 standard
SA272212RF146AM_CSF (TopPhase)
SA272213RF204AM_CSF (TopPhase)
SA272214RF202AM_CSF (TopPhase)
SA272215RF201AM_CSF (TopPhase)
SA272216RF205AM_CSF (TopPhase)
SA272217RF203AM_CSF (TopPhase)
SA272218RF145AM_CSF (TopPhase)
SA272219RF148AM_CSF (TopPhase)
SA272220RF147AM_CSF (TopPhase)
SA272221RF150AM_CSF (TopPhase)
SA272222RF149AM_CSF (TopPhase)
SA272223RF151AM_CSF (TopPhase)
SA272224RF200AM_CSF (TopPhase)
SA272225RF219AM_Serum (TopPhase)
SA272226RF220AM_Serum (TopPhase)
SA272227RF162AM_Serum (TopPhase)
SA272228RF218AM_Serum (TopPhase)
SA272229RF165AM_Serum (TopPhase)
SA272230RF221AM_Serum (TopPhase)
SA272231RF166AM_Serum (TopPhase)
SA272232RF164AM_Serum (TopPhase)
SA272233RF216AM_Serum (TopPhase)
SA272234RF217AM_Serum (TopPhase)
SA272235RF163AM_Serum (TopPhase)
SA272236RF155PM_CSF (TopPhase)
SA272237RF154PM_CSF (TopPhase)
SA272238RF153PM_CSF (TopPhase)
SA272239RF157PM_CSF (TopPhase)
SA272240RF156PM_CSF (TopPhase)
SA272241RF158PM_CSF (TopPhase)
SA272242RF152PM_CSF (TopPhase)
SA272243RF222PM_Serum (TopPhase)
SA272244RF228PM_Serum (TopPhase)
SA272245RF227PM_Serum (TopPhase)
SA272246RF226PM_Serum (TopPhase)
SA272247RF225PM_Serum (TopPhase)
SA272248RF224PM_Serum (TopPhase)
SA272249RF223PM_Serum (TopPhase)
SA272250RF209PM_Serum (TopPhase)
SA272251RF170PM_Serum (TopPhase)
SA272252RF206PM_Serum (TopPhase)
SA272253RF207PM_Serum (TopPhase)
SA272254RF171PM_Serum (TopPhase)
SA272255RF169PM_Serum (TopPhase)
SA272256RF167PM_Serum (TopPhase)
SA272257RF168PM_Serum (TopPhase)
SA272258RF210PM_Serum (TopPhase)
SA272259RF208PM_Serum (TopPhase)
SA272260RF212PM_Serum (TopPhase)
SA272261RF211PM_Serum (TopPhase)
SA272262RF215Apool CSF RF200-212 01x_A
SA272263RF215Bpool CSF RF200-212 01x_B
SA272264RF214pool CSF RF200-212 03x
SA272265RF213Apool CSF RF200-212 1x_A
SA272266RF213Bpool CSF RF200-212 1x_B
SA272267RF213Cpool CSF RF200-212 1x_C
SA272268RF161Apool RF159-172 01x_A
SA272269RF161Bpool RF159-172 01x_B
SA272270RF161Cpool RF159-172 01x_C
SA272271RF160Apool RF159-172 03x_A
SA272272RF160Bpool RF159-172 03x_B
SA272273RF159Apool RF159-172 1x_A
SA272274RF159Bpool RF159-172 1x_B
SA272275RF159Cpool RF159-172 1x_C
SA272276RF174Apool RF176-185 01x_A
SA272277RF174Bpool RF176-185 01x_B
SA272278RF174Cpool RF176-185 01x_C
SA272279RF173Apool RF176-185 03x_A
SA272280RF173Bpool RF176-185 03x_B
SA272281RF172Apool RF176-185 1x_A
SA272282RF172Bpool RF176-185 1x_B
SA272283RF172Cpool RF176-185 1x_C
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Collection ID:CO002805
Collection Summary:All animal studies were performed under the protocol approved by the Institutional Animal Care and Use Committee (IACUC) of Boston Children’s Hospital (BCH). All mice were housed in a 12h light-dark cycle with ad libitum access to food and water. CSF, eCSF, was collected from the cisterna magna of the pup embryos and mother, and centrifuged at 5,000g for 10 min. at 4 °C to remove any tissue debris. CSF samples were kept on ice and analyzed the same day as collection.
Sample Type:CSF


Treatment ID:TR002821
Treatment Summary:Mice (CD-1 males) kept in circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off).

Sample Preparation:

Sampleprep ID:SP002818
Sampleprep Summary:CSF was collected from adult (3 months old) wild-type CD1 mice. Samples were placed on wet ice, then spun 1000xg for 10 minutes at 4C. The supernatant was collected. Per condition, 5-10µL of fresh, cleared CSF or 5µl serum was extracted in 4:6:3 chlorophorm:methanol:water mixture supplemented with isotopically labeled T3 and T4 (Cambridge Isotope Laboratories, CLM-7185-C and CLM-8931-PK ) as well as isotopically labelled 17 amino acids and isotopically labelled reduced glutathione (Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). After centrifugation for 10 min at maximum speed on a benchtop centrifuge (Eppendorf) the top, hydrophilic layer (top phase) was transferred to a new tube, dried using a nitrogen dryer and reconstituted in 20 µl water (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. A small amount of each sample was pooled and serially diluted 3- and 10-fold to be used as quality controls throughout the run of each batch. I calibration curve of unlabeled T3 and T4 standards was run per experiment for concentration calculations.

Combined analysis:

Analysis ID AN004389
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Ascentis Express C18 (150 x 2.1mm,2.7um)
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Units nM


Chromatography ID:CH003292
Chromatography Summary:Ascentis Express C18 HPLC column (2.7 μm × 15 cm × 2.1 mm; Sigma Aldrich).
Instrument Name:Thermo Vanquish
Column Name:Ascentis Express C18 (150 x 2.1mm,2.7um)
Column Temperature:30
Flow Gradient:0–5 min: gradient was 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:0.250 ml/min
Solvent A:water, 0.1% formic acid
Solvent B:acetonitrile, 0.1% formic acid
Chromatography Type:Reversed phase


MS ID:MS004138
Analysis ID:AN004389
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Comments:MS data acquisition was performed using a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe (Thermo Fisher Scientific, San Jose, CA) and was performed at a narrow scan in positive mode (m/z = 600-800) for more specific detection of thyroxine hormones, the resolution was set at 70,000, the AGC target was 5x105, and the max IT was 100 msec. HESI conditions were: Sheath gas flow rate: 40; Aug gas flow rate: 10; Sweet gas flow rate: 0; Spray voltage: 3.5kV (pos), 2.8kV (neg); Capillary temperature: 380ºC; S-lens RF: 60; Aux gas heater temperature: 420 ºC.