Summary of Study ST002286

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 PR001466. The data can be accessed directly via it's Project DOI: 10.21228/M8799K 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 IDST002286
Study TitlePolyI:C Metabolome changes in liver, CSF, serum, and embryonic CSF and liver
Study SummaryTargeted MS analysis of maternal liver, CSF, serum, and embryonic CSF and liver, with saline and PolyI:C administrated to mother.
Institute
Boston Children's Hospital, Harvard Medical School
LaboratoryKanarek Lab
Last NamePetrova
First NameBoryana
AddressEnders 1116.2 300 Longwood Ave
EmailBoryana.Petrova@childrens.harvard.edu
Phone6179197352
Submit Date2022-09-25
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2022-10-10
Release Version1
Boryana Petrova Boryana Petrova
https://dx.doi.org/10.21228/M8799K
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR001466
Project DOI:doi: 10.21228/M8799K
Project Title:Maternal Immune Activation Resource for differences in CSF and Serum metabolomes of maternal mice with and without PolyI:C
Project Summary:This study is part of an investigative series into metabolome composition changes of pregnant mice with and without PolyI:C.
Institute:Boston Childrens Hospital
Last Name:Petrova
First Name:Boryana
Address:300 Longwood Av, Boston, MA, 2115, USA
Email:boryana.petrova@childrens.harvard.edu
Phone:6173557433

Subject:

Subject ID:SU002372
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 Factor
SA21909417CSF10 PolyIC
SA21909510CSF2 PolyIC
SA21909611CSF3 saline
SA21909712CSF4 PolyIC
SA21909813CSF5 saline
SA21909914CSF6 PolyIC
SA21910015CSF7 saline
SA21910116CSF8 PolyIC
SA21910224eC-1
SA21910325eC-2
SA21910426eC-3
SA21910527eC-4
SA21910628eC-5
SA21910729eC-6
SA21910830eC-7
SA21910940eL-1
SA21911048eL-10
SA21911141eL-2
SA21911242eL-3
SA21911343eL-4
SA21911444eL-5
SA21911545eL-6
SA21911646eL-7
SA21911747eL-8
SA21911831mL-1
SA21911939mL-10
SA21912032mL-2
SA21912133mL-3
SA21912234mL-4
SA21912335mL-5
SA21912436mL-6
SA21912537mL-7
SA21912638mL-8
SA21913618mock 1
SA21913719mock 2
SA21913820mock 3
SA21913921mock 5
SA21914022mock 6
SA21914123mock 7
SA2191271mSer1
SA2191289mSer10
SA2191292mSer2
SA2191303mSer3
SA2191314mSer4
SA2191325mSer5
SA2191336mSer6
SA2191347mSer7
SA2191358mSer8
Showing results 1 to 48 of 48

Collection:

Collection ID:CO002365
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 was collected from the cisterna magna 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. Blood samples were coagulated and centrifuged. Liver and kidney were collected and flash frozen. Tissue chunks were cut on a glass plate while kept chilled on top of dry ice.
Collection Protocol Comments:Liver, Serum included
Sample Type:CSF

Treatment:

Treatment ID:TR002384
Treatment Summary:For polyI:C experiments: Pregnant female mice were injected intraperitoneally (route of administration) with a single dose of 20 mg/kg polyI:C (sigma aldrich) and controls will receive an injection of 0.9% saline embryonic day 12.5. Samples were collected either 3hrs or 48hrs post injection.

Sample Preparation:

Sampleprep ID:SP002378
Sampleprep Summary:Per condition, 5uL of maternal serum, CSF, were extracted by brief sonication in 200 μl 80% methanol, supplemented with isotopically labeled internal standards (17 amino acids and reduced glutathione, Cambridge Isotope Laboratories, MSK-A2-1.2 and CNLM-6245-10). 10uL Embryonic CSF (eCSF) was extracted per condition using the previously described buffer quantity, and the flash frozen liver chunks were extracted in 300uL of the previously described buffer. After centrifugation for 10min. at maximum speed on a benchtop centrifuge (Eppendorf) the cleared supernatant from CSF and eCSF was dried using a nitrogen dryer. Samples were reconstituted in LCMS water by brief sonication. Extracted metabolites were spun again and cleared supernatant was transferred in LC-MS microvials. Serum and liver chunks followed the same protocol, except that an additional 20-minute centrifugation was administered, and homogenization for 5 minutes was administered to liver chunks. Final LCMS water reconstitution values for tissue type were 50uL (maternal serum), 15uL (maternal CSF and eCSF), and 100 uL (liver chunks). A small amount of each sample was pooled and serially diluted 3 and 10-fold to be used as quality controls throughout the batch run. Two microliters (equivalent to 0.2 ul of CSF) of reconstituted sample were injected into a ZIC-pHILIC 150 × 2.1 mm (5 µm particle size) column (EMD Millipore) operated on a Dionex UltiMate 3000 UPLC system (Thermo Fisher Scientific). Chromatographic separation was achieved using the following conditions: buffer A was acetonitrile; buffer B was 20 mM ammonium carbonate, 0.1% ammonium hydroxide. Gradient conditions were: linear gradient from 20% to 80% B; 20–20.5 min: from 80% to 20% B; 20.5–28 min: hold at 20% B. The column oven and autosampler tray were held at 25 °C and 4 °C, respectively. The MS data acquisition was on a QExactive benchtop orbitrap mass spectrometer equipped with an Ion Max source and a HESI II probe and was performed 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. For tSIM scans, the resolution was set at 70,000, the AGC target was 1x105, and the max IT was 100 msec. Relative quantitation of polar metabolites was performed with TraceFinder 4.1 (Thermo Fisher Scientific) using a 5 ppm mass tolerance and referencing an in-house library of chemical standards. Pooled samples and fractional dilutions were prepared as quality controls and only those metabolites were taken for further analysis, for which the correlation between the dilution factor and the peak area was >0.95 (high confidence metabolites).

Combined analysis:

Analysis ID AN003738
Analysis type MS
Chromatography type HILIC
Chromatography system Thermo Vanquish
Column SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Plus Orbitrap
Ion Mode UNSPECIFIED
Units ppm

Chromatography:

Chromatography ID:CH002769
Chromatography Summary:ZIC-pHILIC
Instrument Name:Thermo Vanquish
Column Name:SeQuant ZIC-pHILIC (150 x 2.1mm,5um)
Chromatography Type:HILIC

MS:

MS ID:MS003486
Analysis ID:AN003738
Instrument Name:Thermo Q Exactive Plus Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:HESI
Ion Mode:UNSPECIFIED
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