Summary of study ST001745

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 PR001118. The data can be accessed directly via it's Project DOI: 10.21228/M86404 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 IDST001745
Study TitleMetabolomic profiling of the rat hippocampus across developmental ages and after learning
Study TypeDevelopmental study
Study SummaryLittle is known about how the hippocampal metabolomic profile changes across development and in response to learning at different ages. To fill this knowledge gap, we employed an untargeted metabolomic analyses in rats to determine how the hippocampal metabolome changes over the course of post-natal development under basal conditions and following inhibitory avoidance (IA) training, an aversive episodic event. We found that unique metabolomic profiles accompany learning at different ages. Subsequent biochemical and behavioral studies based on unique metabolomic regulations in the infant hippocampus established that infantile learning selectively recruits the glutathione-mediated antioxidant defenses for the formation of infantile memory.
Institute
New York University
DepartmentCenter for Neural Science (NYU)
LaboratoryCristina Alberini
Last NameBessieres
First NameBenjamin
Address4 Washington Place, Room 623
Emailbjb11@nyu.edu
Phone6315684274
Submit Date2021-03-26
Num Groups8
Total Subjects52
Num Males35
Num Females17
Raw Data AvailableYes
Raw Data File Type(s).xls
Analysis Type DetailLC-MS
Release Date2021-05-01
Release Version1
Benjamin Bessieres Benjamin Bessieres
https://dx.doi.org/10.21228/M86404
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:


Project:

Project ID:PR001118
Project DOI:doi: 10.21228/M86404
Project Title:Metabolomic profiling of the rat hippocampus across developmental ages and after learning.
Project Type:Neuroscience
Project Summary:The metabolic mechanisms underlying the formation of early-life episodic memories remain poorly characterized. To fill this knowledge gap, we employed an untargeted metabolomic analysis in rats to determine how the hippocampal metabolome changes over the course of post-natal development under basal conditions and following inhibitory avoidance (IA) training, an aversive episodic event. We found that unique metabolomic profiles accompany learning at different ages. Subsequent biochemical and behavioral studies based on unique metabolomic regulations in the infant hippocampus established that infantile learning selectively recruits the glutathione-mediated antioxidant defenses for the formation of infantile memory.
Institute:New York University
Department:Center for Neural Science (NYU)
Laboratory:Cristina Alberini
Last Name:Bessieres
First Name:Benjamin
Address:4 Washington Place, Room 623
Email:bjb11@nyu.edu
Phone:6315684274
Funding Source:NIH

Subject:

Subject ID:SU001822
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116
Genotype Strain:Long Evans
Age Or Age Range:From post-natal day 1 (PN1) to PN80
Weight Or Weight Range:5g-250g
Gender:Male and female
Animal Animal Supplier:Envigo
Animal Housing:Animal facility at NYU
Animal Light Cycle:7am-7pm

Factors:

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

mb_sample_id local_sample_id Treatment
SA163301NYSM-00454naive
SA163302NYSM-00481naive
SA163303NYSM-00482naive
SA163304NYSM-00479naive
SA163305NYSM-00478naive
SA163306NYSM-00476naive
SA163307NYSM-00477naive
SA163308NYSM-00483naive
SA163309NYSM-00492naive
SA163310NYSM-00496naive
SA163311NYSM-00497naive
SA163312NYSM-00498naive
SA163313NYSM-00495naive
SA163314NYSM-00494naive
SA163315NYSM-00475naive
SA163316NYSM-00493naive
SA163317NYSM-00484naive
SA163318NYSM-00480naive
SA163319NYSM-00461naive
SA163320NYSM-00459naive
SA163321NYSM-00458naive
SA163322NYSM-00463naive
SA163323NYSM-00457naive
SA163324NYSM-00460naive
SA163325NYSM-00462naive
SA163326NYSM-00472naive
SA163327NYSM-00455naive
SA163328NYSM-00471naive
SA163329NYSM-00470naive
SA163330NYSM-00469naive
SA163331NYSM-00456naive
SA163332NYSM-00502trained
SA163333NYSM-00504trained
SA163334NYSM-00505trained
SA163335NYSM-00503trained
SA163336NYSM-00501trained
SA163337NYSM-00500trained
SA163338NYSM-00499trained
SA163339NYSM-00489trained
SA163340NYSM-00466trained
SA163341NYSM-00465trained
SA163342NYSM-00467trained
SA163343NYSM-00468trained
SA163344NYSM-00474trained
SA163345NYSM-00464trained
SA163346NYSM-00485trained
SA163347NYSM-00473trained
SA163348NYSM-00490trained
SA163349NYSM-00488trained
SA163350NYSM-00487trained
SA163351NYSM-00486trained
SA163352NYSM-00491trained
Showing results 1 to 52 of 52

Collection:

Collection ID:CO001815
Collection Summary:Rats trained in inhibitory avoidance at PN17, PN24, and PN80, and the untrained (naive) control rats were euthanized by decapitation (1 hour after IA training). Their brains were quickly removed and placed in ice-cold phosphate-buffered saline (1X). Whole hippocampal samples were dissected and immediately snap-frozen in isopentane on dry ice. All samples were stored at -80°C until processing. Frozen samples were shipped in dry ice to Metabolon Inc. (Morrisville, NC, USA) for metabolomic analysis using a proprietary methodology. Extraction of samples was performed using a MicroLab STAR automated liquid handling robot (Hamilton Robotics, Inc., Reno, NV, USA); 450 μL of methanol was added to 100 μo of sample to precipitate proteins. Four recovery standards (DL-2-fluorophenylglycine, tridecanoic acid, cholesterol-d6 and 4-chlorophenylalanine) were added to each sample to determine extraction efficiency. To remove proteins, dissociate small molecules bound to protein, and recover metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation (1300 g for 10 min at room temperature). The resultant supernatants were placed in a TurboVap (Zymark) to remove the organic solvent. Each sample extract was then divided into five equal aliquots, dried under nitrogen, and stored in vacuo prior to metabolomic profiling.
Sample Type:Brain
Collection Method:Brain dissection
Collection Location:New York University
Storage Conditions:-80℃

Treatment:

Treatment ID:TR001835
Treatment Summary:Metabolomic profiling was carried out on hippocampal extracts (five to seven individual replicates) obtained from untrained rats at four early, prepuberal developmental ages [postnatal day 1 (PN1), PN7, PN17 and PN24] and compared to the profile obtained from young adults (PN80). Additionally, the metabolomic profiles of the hippocampus 1 hour after IA training at PN17, PN24, and PN80 were compared with those of age-matched untrained (naive) control rats.

Sample Preparation:

Sampleprep ID:SP001828
Sampleprep Summary:Extraction of samples was performed using a MicroLab STAR automated liquid handling robot (Hamilton Robotics, Inc., Reno, NV, USA); 450 μL of methanol was added to 100 μL of sample to precipitate proteins. Four recovery standards (DL-2-fluorophenylglycine, tridecanoic acid, cholesterol-d6 and 4-chlorophenylalanine) were added to each sample to determine extraction efficiency. To remove proteins, dissociate small molecules bound to protein, and recover metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation (1300 g for 10 min at room temperature). The resultant supernatants were placed in a TurboVap (Zymark) to remove the organic solvent. Each sample extract was then divided into five equal aliquots, dried under nitrogen, and stored in vacuo prior to metabolomic profiling.

Combined analysis:

Analysis ID AN002838 AN002839 AN002840 AN002841
Analysis type MS MS MS MS
Chromatography type Reversed phase Reversed phase Reversed phase HILIC
Chromatography system Waters Acquity Waters Acquity Waters Acquity Waters Acquity
Column Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH C18 (100 x 2mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI ESI Other
MS instrument type Orbitrap Orbitrap Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE POSITIVE NEGATIVE NEGATIVE
Units pmoles/l pmoles/l pmoles/l pmoles/l

Chromatography:

Chromatography ID:CH002101
Chromatography Summary:The first two aliquots were analyzed by two separate reverse-phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI): one aliquot was analyzed using acidic positive-ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient-eluted from a C18 column (2 mm × 100 mm Waters UPLC BEH C18 1.7 µm column held at 40°C) using 5% water and 95% methanol and containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA) at pH 3.5. The second aliquot was also analyzed using acidic positive-ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient-eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA at pH 3.5. A third aliquot was analyzed by RP/UPLC-MS/MS using basic negative-ion mode ESI in a separate dedicated C18 column. The basic extracts were gradient-eluted from the column using methanol (95%) and water (5%) with 6.5 mM ammonium bicarbonate at pH 8.
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH C18 (100 x 2mm, 1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002102
Chromatography Summary:The fourth aliquot was analyzed via negative ionization following elution from a Hydrophilic-Interaction Chromatography (HILIC) column (2.1 mm x 150 mm Waters UPLC BEH Amide, 1.7 µm column held at 40°C) using a mobile phase consisting of 10 mM ammonium formate in 15% water, 5% methanol, 80% acetonitrile (pH 10.8).
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Chromatography Type:HILIC

MS:

MS ID:MS002631
Analysis ID:AN002838
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:One aliquot was analyzed using acidic positive-ion conditions, chromatographically optimized for more hydrophilic compounds. In this method, the extract was gradient-eluted from a C18 column (2.1 mm × 100 mm Waters UPLC BEH C18 1.7 µm column held at 40°C) using 5% water and 95% methanol and containing 0.05% perfluoropentanoic acid (PFPA) and 0.1% formic acid (FA) at pH 3.5.
Ion Mode:POSITIVE
  
MS ID:MS002632
Analysis ID:AN002839
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The second aliquot was also analyzed using acidic positive-ion conditions; however, it was chromatographically optimized for more hydrophobic compounds. In this method, the extract was gradient-eluted from the aforementioned C18 column using methanol, acetonitrile, water, 0.05% PFPA, and 0.01% FA at pH 3.5.
Ion Mode:POSITIVE
  
MS ID:MS002633
Analysis ID:AN002840
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:A third aliquot was analyzed by RP/UPLC-MS/MS using basic negative-ion mode ESI in a separate dedicated C18 column. The basic extracts were gradient-eluted from the column using methanol (95%) and water (5%) with 6.5 mM ammonium bicarbonate at pH 8.
Ion Mode:NEGATIVE
  
MS ID:MS002634
Analysis ID:AN002841
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:Other
MS Comments:The fourth aliquot was analyzed via negative ionization following elution from a Hydrophilic-Interaction Chromatography (HILIC) column (2.1 mm x 150 mm Waters UPLC BEH Amide, 1.7 µm column held at 40°C) using a mobile phase consisting of 10 mM ammonium formate in 15% water, 5% methanol, 80% acetonitrile (pH 10.8).
Ion Mode:NEGATIVE
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