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.
| Study ID | ST002708 |
| Study Title | Levels of central carbon metabolites in choroid plexus as part of natural diurnal variation |
| Study Summary | This 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 |
| Department | Pathology |
| Laboratory | Kanarek Lab |
| Last Name | Petrova |
| First Name | Boryana |
| Address | 330 Longwood Av |
| boryana.petrova@childrens.harvard.edu | |
| Phone | 6173557433 |
| Submit Date | 2023-05-15 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-05-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Diurnal_Cycle |
|---|---|---|
| SA272290 | RF34 | AM 4V_ChP (FB extraction) |
| SA272291 | RF42 | AM 4V_ChP (FB extraction) |
| SA272292 | RF18 | AM 4V_ChP (FB extraction) |
| SA272293 | RF38 | AM 4V_ChP (FB extraction) |
| SA272294 | RF30 | AM 4V_ChP (FB extraction) |
| SA272295 | RF22 | AM 4V_ChP (FB extraction) |
| SA272296 | RF46 | AM 4V_ChP (FB extraction) |
| SA272297 | RF26 | AM 4V_ChP (FB extraction) |
| SA272298 | RF48 | AM 4V_ChP (MetOH extraction) |
| SA272299 | RF44 | AM 4V_ChP (MetOH extraction) |
| SA272300 | RF40 | AM 4V_ChP (MetOH extraction) |
| SA272301 | RF20 | AM 4V_ChP (MetOH extraction) |
| SA272302 | RF28 | AM 4V_ChP (MetOH extraction) |
| SA272303 | RF24 | AM 4V_ChP (MetOH extraction) |
| SA272304 | RF32 | AM 4V_ChP (MetOH extraction) |
| SA272305 | RF36 | AM 4V_ChP (MetOH extraction) |
| SA272306 | RF25 | AM LV_ChP (FB extraction) |
| SA272307 | RF21 | AM LV_ChP (FB extraction) |
| SA272308 | RF33 | AM LV_ChP (FB extraction) |
| SA272309 | RF37 | AM LV_ChP (FB extraction) |
| SA272310 | RF45 | AM LV_ChP (FB extraction) |
| SA272311 | RF41 | AM LV_ChP (FB extraction) |
| SA272312 | RF29 | AM LV_ChP (FB extraction) |
| SA272313 | RF17 | AM LV_ChP (FB extraction) |
| SA272314 | RF43 | AM LV_ChP (MetOH extraction) |
| SA272315 | RF47 | AM LV_ChP (MetOH extraction) |
| SA272316 | RF35 | AM LV_ChP (MetOH extraction) |
| SA272317 | RF31 | AM LV_ChP (MetOH extraction) |
| SA272318 | RF23 | AM LV_ChP (MetOH extraction) |
| SA272319 | RF27 | AM LV_ChP (MetOH extraction) |
| SA272320 | RF19 | AM LV_ChP (MetOH extraction) |
| SA272321 | RF39 | AM LV_ChP (MetOH extraction) |
| SA272322 | RF58 | PM 4V_ChP (FB extraction) |
| SA272323 | RF66 | PM 4V_ChP (FB extraction) |
| SA272324 | RF54 | PM 4V_ChP (FB extraction) |
| SA272325 | RF70 | PM 4V_ChP (FB extraction) |
| SA272326 | RF50 | PM 4V_ChP (FB extraction) |
| SA272327 | RF78 | PM 4V_ChP (FB extraction) |
| SA272328 | RF74 | PM 4V_ChP (FB extraction) |
| SA272329 | RF62 | PM 4V_ChP (FB extraction) |
| SA272330 | RF52 | PM 4V_ChP (MetOH extraction) |
| SA272331 | RF68 | PM 4V_ChP (MetOH extraction) |
| SA272332 | RF72 | PM 4V_ChP (MetOH extraction) |
| SA272333 | RF76 | PM 4V_ChP (MetOH extraction) |
| SA272334 | RF80 | PM 4V_ChP (MetOH extraction) |
| SA272335 | RF60 | PM 4V_ChP (MetOH extraction) |
| SA272336 | RF56 | PM 4V_ChP (MetOH extraction) |
| SA272337 | RF64 | PM 4V_ChP (MetOH extraction) |
| SA272338 | RF53 | PM LV_ChP (FB extraction) |
| SA272339 | RF77 | PM LV_ChP (FB extraction) |
| SA272340 | RF73 | PM LV_ChP (FB extraction) |
| SA272341 | RF65 | PM LV_ChP (FB extraction) |
| SA272342 | RF61 | PM LV_ChP (FB extraction) |
| SA272343 | RF57 | PM LV_ChP (FB extraction) |
| SA272344 | RF69 | PM LV_ChP (FB extraction) |
| SA272345 | RF49 | PM LV_ChP (FB extraction) |
| SA272346 | RF59 | PM LV_ChP (MetOH extraction) |
| SA272347 | RF63 | PM LV_ChP (MetOH extraction) |
| SA272348 | RF67 | PM LV_ChP (MetOH extraction) |
| SA272349 | RF55 | PM LV_ChP (MetOH extraction) |
| SA272350 | RF71 | PM LV_ChP (MetOH extraction) |
| SA272351 | RF75 | PM LV_ChP (MetOH extraction) |
| SA272352 | RF79 | PM LV_ChP (MetOH extraction) |
| SA272353 | RF51 | PM LV_ChP (MetOH extraction) |
| SA272354 | RF86_A | pool FB 01x_A |
| SA272355 | RF86_B | pool FB 01x_B |
| SA272356 | RF85 | pool FB 03x |
| SA272357 | RF84_C | pool FB 1x |
| SA272358 | RF84_A | pool FB 1x_A |
| SA272359 | RF84_B | pool FB 1x_B |
| SA272360 | RF84_D | pool FB 1x_C |
| SA272361 | RF84 | pool FB 1x_D |
| SA272362 | RF83_A | pool MetOH 01x_A |
| SA272363 | RF83_B | pool MetOH 01x_B |
| SA272364 | RF82 | pool MetOH 03x |
| SA272365 | RF81_A | pool MetOH 1x_A |
| SA272366 | RF81_B | pool MetOH 1x_B |
| SA272367 | RF81_C | pool MetOH 1x_C |
| SA272368 | RF81_D | pool MetOH 1x_D |
| SA272369 | RF81_E | pool MetOH 1x_E |
| Showing results 1 to 80 of 80 |
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 |
