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.
Study ID | ST002286 |
Study Title | PolyI:C Metabolome changes in liver, CSF, serum, and embryonic CSF and liver |
Study Summary | Targeted 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 |
Laboratory | Kanarek Lab |
Last Name | Petrova |
First Name | Boryana |
Address | Enders 1116.2 300 Longwood Ave |
Boryana.Petrova@childrens.harvard.edu | |
Phone | 6179197352 |
Submit Date | 2022-09-25 |
Raw Data Available | Yes |
Raw Data File Type(s) | raw(Thermo) |
Analysis Type Detail | LC-MS |
Release Date | 2022-10-10 |
Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
---|---|---|
SA219094 | 17 | CSF10 PolyIC |
SA219095 | 10 | CSF2 PolyIC |
SA219096 | 11 | CSF3 saline |
SA219097 | 12 | CSF4 PolyIC |
SA219098 | 13 | CSF5 saline |
SA219099 | 14 | CSF6 PolyIC |
SA219100 | 15 | CSF7 saline |
SA219101 | 16 | CSF8 PolyIC |
SA219102 | 24 | eC-1 |
SA219103 | 25 | eC-2 |
SA219104 | 26 | eC-3 |
SA219105 | 27 | eC-4 |
SA219106 | 28 | eC-5 |
SA219107 | 29 | eC-6 |
SA219108 | 30 | eC-7 |
SA219109 | 40 | eL-1 |
SA219110 | 48 | eL-10 |
SA219111 | 41 | eL-2 |
SA219112 | 42 | eL-3 |
SA219113 | 43 | eL-4 |
SA219114 | 44 | eL-5 |
SA219115 | 45 | eL-6 |
SA219116 | 46 | eL-7 |
SA219117 | 47 | eL-8 |
SA219118 | 31 | mL-1 |
SA219119 | 39 | mL-10 |
SA219120 | 32 | mL-2 |
SA219121 | 33 | mL-3 |
SA219122 | 34 | mL-4 |
SA219123 | 35 | mL-5 |
SA219124 | 36 | mL-6 |
SA219125 | 37 | mL-7 |
SA219126 | 38 | mL-8 |
SA219136 | 18 | mock 1 |
SA219137 | 19 | mock 2 |
SA219138 | 20 | mock 3 |
SA219139 | 21 | mock 5 |
SA219140 | 22 | mock 6 |
SA219141 | 23 | mock 7 |
SA219127 | 1 | mSer1 |
SA219128 | 9 | mSer10 |
SA219129 | 2 | mSer2 |
SA219130 | 3 | mSer3 |
SA219131 | 4 | mSer4 |
SA219132 | 5 | mSer5 |
SA219133 | 6 | mSer6 |
SA219134 | 7 | mSer7 |
SA219135 | 8 | mSer8 |
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 |