Summary of Study ST002772

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 PR001729. The data can be accessed directly via it's Project DOI: 10.21228/M86X4K 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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002772
Study TitleDay-night fluctuations in Cerebrospinal fluid metabolomics
Study TypeCircadian (Naïve animals)
Study SummaryThis study was designed to investigate whether the molecular drivers underlying the diurnal fluctuation of CSF secretion rate could be found in either the choroid plexus tissue itself and/or in the CSF surrounding it. Male Sprague-Dawley rats, kept in light-controlled 12:12 conditions, presented with diurnally modulated CSF metabolite composition. This change was accompanied with differential expression of 2778 genes within the choroid plexus, with several plasma membrane transporters and CLOCK-associated genes diurnally modulated.
Institute
University of Copenhagen
DepartmentDepartment of Neuroscience
LaboratoryMacAulay Group
Last NameEdelbo
First NameBeatriche
AddressBlegdamsvej 3B
Emailbeatriche.henriksen@sund.ku.dk
Phone+4527697585
Submit Date2023-07-04
Num Groups2
Total Subjects25
Num Males25
Study Comments2 night animals were excluded due to comments regarding sampling/behavior (N4 and N11)
PublicationsDay-night fluctuations in choroid plexus transcriptomics and cerebrospinal fluid metabolomics
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-07-25
Release Version1
Beatriche Edelbo Beatriche Edelbo
https://dx.doi.org/10.21228/M86X4K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001729
Project DOI:doi: 10.21228/M86X4K
Project Title:Day-night fluctuations in choroid plexus transcriptomics and CSF metabolomics
Project Type:LC-MS quantitative
Project Summary:Analysis of metabolites within CSF of male Sprague-Dawley rats 8 hours after light on (ZT8) and 8 hours after light off (ZT20)
Institute:University of Copenhagen
Department:Department of Neuroscience
Laboratory:MacAulay Group
Last Name:Edelbo
First Name:Beatriche
Address:Blegdamsvej 3B, building 24.6
Email:beatriche.henriksen@sund.ku.dk
Phone:27697585
Funding Source:Lundbeck Foundation (ascending investigator grant, R313-2019-735, and R276-2018-403 to Nanna MacAulay )
Publications:Day-night fluctuations in choroid plexus transcriptomics and cerebrospinal fluid metabolomics
Contributors:Beatriche L. Edelbo, Søren N. Andreassen, Annette B. Steffensen, Nanna MacAulay

Subject:

Subject ID:SU002879
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Age Or Age Range:9 weeks
Weight Or Weight Range:380-430
Gender:Male
Animal Animal Supplier:Janvier
Animal Housing:Grouped
Animal Light Cycle:12:12 (normal phase)
Animal Feed:Ad libitum normal diet
Animal Water:Ad libitum
Species Group:Sprague-Dawley

Factors:

Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)

mb_sample_id local_sample_id factor
SA294432N2Dark phase sample
SA294433N4Dark phase sample
SA294434N3Dark phase sample
SA294435N10Dark phase sample
SA294436?N1Dark phase sample
SA294437N1Dark phase sample
SA294438N5Dark phase sample
SA294439N6Dark phase sample
SA294440?N3Dark phase sample
SA294441?N2Dark phase sample
SA294442N9Dark phase sample
SA294443?N4Dark phase sample
SA294444N7Dark phase sample
SA294445N8Dark phase sample
SA294446D8Light phase sample
SA294447D9Light phase sample
SA294448D7Light phase sample
SA294449D4Light phase sample
SA294450D10Light phase sample
SA294451D6Light phase sample
SA294452D11Light phase sample
SA294453D1Light phase sample
SA294454D2Light phase sample
SA294455D5Light phase sample
SA294456D3Light phase sample
SA294457QC2Pooled samples - quality control
SA294458QC1Pooled samples - quality control
SA294459QC3Pooled samples - quality control
SA294460QC6Pooled samples - quality control
SA294461QCPooled samples - quality control
SA294462QC5Pooled samples - quality control
SA294463QC4Pooled samples - quality control
Showing results 1 to 32 of 32

Collection:

Collection ID:CO002872
Collection Summary:CSF was collected during natural light or dark phase (2 AM/PM) via cisterna magna punctur, spun down 10 minutes then put on dry ice until storage at -80C.
Collection Protocol Filename:methods.txt
Sample Type:Cerebrospinal fluid
Storage Conditions:-80℃
Collection Vials:Eppendorf tube
Storage Vials:Microtube, 72-730-006, Sarstedt AG & Co
Collection Tube Temp:4

Treatment:

Treatment ID:TR002888
Treatment Summary:No treatment, natural light and dark phase, anesthesia during sampling 6 mg/ml xylazine + 60 mg/ml ketamine. Animals was housed at light-controlled facility a minimum of 1½ weeks prior to experimentation.

Sample Preparation:

Sampleprep ID:SP002885
Sampleprep Summary:No sample prep was done after freezing.

Combined analysis:

Analysis ID AN004512
Analysis type MS
Chromatography type Reversed phase
Chromatography system Thermo Vanquish
Column Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive HF MS
Ion Mode UNSPECIFIED
Units Peak area

Chromatography:

Chromatography ID:CH003389
Chromatography Summary:HILIC and Reverse-phase was performed by MS-Omics (Denmark). Data recieved includ raw spectrometry files and combined data from the negative and positive mode (supplied in data section)
Chromatography Comments:For Reverse phase column was Water acquity HSS T3 (2.1x150 mm, 1.7 um) coupled with a high-resolution quadrupole-orbitrap mass spectrometer
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:30
Flow Gradient:-
Flow Rate:300 uL/minute
Solvent A:100% water; 10 mM ammonium formate; 0.1% formic acid (pH 3.1)
Solvent B:100% methanol; 10 mM ammonium formate; 0.1% formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS004259
Analysis ID:AN004512
Instrument Name:Thermo Q Exactive HF MS
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:iterative data-dependent acquisition, run to Data was processed using Compound Discoverer 3.2 (ThermoFisher Scientific) and Skyline.
Ion Mode:UNSPECIFIED
  logo