Summary of Study ST002708

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 PR001678. The data can be accessed directly via it's Project DOI: 10.21228/M8T146 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

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 IDST002708
Study TitleLevels of central carbon metabolites in choroid plexus as part of natural diurnal variation
Study SummaryThis study employs targeted LC-MS analysis of choroid plexus (ChP) tissue to assess relative changes in the levels of intermediates from the central carbon metabolism, with additional attention to mitochondrial energy precursors (ATP/ADP, NAD(P) and NAD(P)H) at two time points in the diurnal cycle. For this purpose, 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). Two different ChP tissues were collected for analysis (LV - left ventricle and 4V - 4th ventricle). Also two separate extractions were performed: 80% MetOH based ("MetOH" study factor) and FB (MetOH with Na-ascorbate and Na-acetate additives, "FB" study factor). The two extractions are optimal for central carbon metabolites or NAD(P)/H respectively.
Institute
Boston Children's Hospital
DepartmentPathology
LaboratoryKanarek Lab
Last NamePetrova
First NameBoryana
Address330 Longwood Av
Emailboryana.petrova@childrens.harvard.edu
Phone6173557433
Submit Date2023-05-15
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-05-28
Release Version1
Boryana Petrova Boryana Petrova
https://dx.doi.org/10.21228/M8T146
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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
Department:Pathology
Laboratory:Kanarek Lab
Last Name:Petrova
First Name:Boryana
Address:300 Longwood Av, Boston, MA, 2115, USA
Email:boryana.petrova@childrens.harvard.edu
Phone:6173557433
Contributors:Boryana Petrova, Ryann Fame

Subject:

Subject ID:SU002813
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 Diurnal_Cycle
SA272290RF34AM 4V_ChP (FB extraction)
SA272291RF42AM 4V_ChP (FB extraction)
SA272292RF18AM 4V_ChP (FB extraction)
SA272293RF38AM 4V_ChP (FB extraction)
SA272294RF30AM 4V_ChP (FB extraction)
SA272295RF22AM 4V_ChP (FB extraction)
SA272296RF46AM 4V_ChP (FB extraction)
SA272297RF26AM 4V_ChP (FB extraction)
SA272298RF48AM 4V_ChP (MetOH extraction)
SA272299RF44AM 4V_ChP (MetOH extraction)
SA272300RF40AM 4V_ChP (MetOH extraction)
SA272301RF20AM 4V_ChP (MetOH extraction)
SA272302RF28AM 4V_ChP (MetOH extraction)
SA272303RF24AM 4V_ChP (MetOH extraction)
SA272304RF32AM 4V_ChP (MetOH extraction)
SA272305RF36AM 4V_ChP (MetOH extraction)
SA272306RF25AM LV_ChP (FB extraction)
SA272307RF21AM LV_ChP (FB extraction)
SA272308RF33AM LV_ChP (FB extraction)
SA272309RF37AM LV_ChP (FB extraction)
SA272310RF45AM LV_ChP (FB extraction)
SA272311RF41AM LV_ChP (FB extraction)
SA272312RF29AM LV_ChP (FB extraction)
SA272313RF17AM LV_ChP (FB extraction)
SA272314RF43AM LV_ChP (MetOH extraction)
SA272315RF47AM LV_ChP (MetOH extraction)
SA272316RF35AM LV_ChP (MetOH extraction)
SA272317RF31AM LV_ChP (MetOH extraction)
SA272318RF23AM LV_ChP (MetOH extraction)
SA272319RF27AM LV_ChP (MetOH extraction)
SA272320RF19AM LV_ChP (MetOH extraction)
SA272321RF39AM LV_ChP (MetOH extraction)
SA272322RF58PM 4V_ChP (FB extraction)
SA272323RF66PM 4V_ChP (FB extraction)
SA272324RF54PM 4V_ChP (FB extraction)
SA272325RF70PM 4V_ChP (FB extraction)
SA272326RF50PM 4V_ChP (FB extraction)
SA272327RF78PM 4V_ChP (FB extraction)
SA272328RF74PM 4V_ChP (FB extraction)
SA272329RF62PM 4V_ChP (FB extraction)
SA272330RF52PM 4V_ChP (MetOH extraction)
SA272331RF68PM 4V_ChP (MetOH extraction)
SA272332RF72PM 4V_ChP (MetOH extraction)
SA272333RF76PM 4V_ChP (MetOH extraction)
SA272334RF80PM 4V_ChP (MetOH extraction)
SA272335RF60PM 4V_ChP (MetOH extraction)
SA272336RF56PM 4V_ChP (MetOH extraction)
SA272337RF64PM 4V_ChP (MetOH extraction)
SA272338RF53PM LV_ChP (FB extraction)
SA272339RF77PM LV_ChP (FB extraction)
SA272340RF73PM LV_ChP (FB extraction)
SA272341RF65PM LV_ChP (FB extraction)
SA272342RF61PM LV_ChP (FB extraction)
SA272343RF57PM LV_ChP (FB extraction)
SA272344RF69PM LV_ChP (FB extraction)
SA272345RF49PM LV_ChP (FB extraction)
SA272346RF59PM LV_ChP (MetOH extraction)
SA272347RF63PM LV_ChP (MetOH extraction)
SA272348RF67PM LV_ChP (MetOH extraction)
SA272349RF55PM LV_ChP (MetOH extraction)
SA272350RF71PM LV_ChP (MetOH extraction)
SA272351RF75PM LV_ChP (MetOH extraction)
SA272352RF79PM LV_ChP (MetOH extraction)
SA272353RF51PM LV_ChP (MetOH extraction)
SA272354RF86_Apool FB 01x_A
SA272355RF86_Bpool FB 01x_B
SA272356RF85pool FB 03x
SA272357RF84_Cpool FB 1x
SA272358RF84_Apool FB 1x_A
SA272359RF84_Bpool FB 1x_B
SA272360RF84_Dpool FB 1x_C
SA272361RF84pool FB 1x_D
SA272362RF83_Apool MetOH 01x_A
SA272363RF83_Bpool MetOH 01x_B
SA272364RF82pool MetOH 03x
SA272365RF81_Apool MetOH 1x_A
SA272366RF81_Bpool MetOH 1x_B
SA272367RF81_Cpool MetOH 1x_C
SA272368RF81_Dpool MetOH 1x_D
SA272369RF81_Epool MetOH 1x_E
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Collection:

Collection ID:CO002806
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). Mice (CD-1 males) kept in circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off) aged 8 weeks (N =16 at each time—9 a.m. and 9 p.m.), were decapitated and brain tissue was immediately dissected and frozen on dry ice. ChP were extracted by brief sonication in either 200µl 80% LC/MS-grade methanol extraction solvent or 200µl of ”FB” extraction solvent (80% LC/MS-grade methanol, 20% 25 mM Ammonium Acetate and 2.5 mM Na-Ascorbate prepared in LC/MS water and supplemented with isotopically labeled internal standards (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 cleared supernatant was 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.
Sample Type:Choroid Plexus

Treatment:

Treatment ID:TR002822
Treatment Summary:Mice (CD-1 males) kept in circadian cabinet housing with 12-hour light cycle (7 a.m. on/ 7 p.m. off). Two tissues were examined (left ventricle choroid plexus and 4th ventricle choroid plexus). Two separate extractions were performed to capture a wider set of metabolites.

Sample Preparation:

Sampleprep ID:SP002819
Sampleprep Summary:ChP were extracted by brief sonication in either 200µl 80% LC/MS-grade methanol extraction solvent or 200µl of ”FB” extraction solvent (80% LC/MS-grade methanol, 20% 25 mM Ammonium Acetate and 2.5 mM Na-Ascorbate prepared in LC/MS water and supplemented with isotopically labeled internal standards (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 cleared supernatant was 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.

Combined analysis:

Analysis ID AN004390
Analysis type MS
Chromatography type HILIC
Chromatography system Vanquish™ Flex UHPLC
Column Merck 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:CH003293
Chromatography Summary:ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore) operated on a Vanquish™ Flex UHPLC Systems (Thermo Fisher Scientific, San Jose, CA).
Instrument Name:Vanquish™ Flex UHPLC
Column Name:Merck SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Column Temperature:25
Flow Gradient:linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B
Flow Rate:0.150µl/min
Solvent A:100% acetonitrile
Solvent B:100% water; 20 mM ammonium carbonate; 0.1% ammonium hydroxide
Chromatography Type:HILIC

MS:

MS ID:MS004139
Analysis ID:AN004390
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
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 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 1x106, 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 thyroxine hormones, the resolution was set at 70,000, the AGC target was 5x105, and the max IT was 100 msec. For polar metabolites HESI conditions were: Sheath gas frow rate: 35; Aug gas flow rate: 8; Sweet gas flow rate: 1; Spray voltage: 3.5kV (pos), 2.8kV (neg); Capillary temperature: 320ºC; S-lens RF: 50; Aux gas heater temperature: 350 ºC.
Ion Mode:UNSPECIFIED
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