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.

Study ID	ST001745
Study Title	Metabolomic profiling of the rat hippocampus across developmental ages and after learning
Study Type	Developmental study
Study Summary	Little 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
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
Submit Date	2021-03-26
Num Groups	8
Total Subjects	52
Num Males	35
Num Females	17
Raw Data Available	Yes
Analysis Type Detail	LC-MS
Release Date	2021-05-01
Release Version	1

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
SA163301	NYSM-00454	naive
SA163302	NYSM-00481	naive
SA163303	NYSM-00482	naive
SA163304	NYSM-00479	naive
SA163305	NYSM-00478	naive
SA163306	NYSM-00476	naive
SA163307	NYSM-00477	naive
SA163308	NYSM-00483	naive
SA163309	NYSM-00492	naive
SA163310	NYSM-00496	naive
SA163311	NYSM-00497	naive
SA163312	NYSM-00498	naive
SA163313	NYSM-00495	naive
SA163314	NYSM-00494	naive
SA163315	NYSM-00475	naive
SA163316	NYSM-00493	naive
SA163317	NYSM-00484	naive
SA163318	NYSM-00480	naive
SA163319	NYSM-00461	naive
SA163320	NYSM-00459	naive
SA163321	NYSM-00458	naive
SA163322	NYSM-00463	naive
SA163323	NYSM-00457	naive
SA163324	NYSM-00460	naive
SA163325	NYSM-00462	naive
SA163326	NYSM-00472	naive
SA163327	NYSM-00455	naive
SA163328	NYSM-00471	naive
SA163329	NYSM-00470	naive
SA163330	NYSM-00469	naive
SA163331	NYSM-00456	naive
SA163332	NYSM-00502	trained
SA163333	NYSM-00504	trained
SA163334	NYSM-00505	trained
SA163335	NYSM-00503	trained
SA163336	NYSM-00501	trained
SA163337	NYSM-00500	trained
SA163338	NYSM-00499	trained
SA163339	NYSM-00489	trained
SA163340	NYSM-00466	trained
SA163341	NYSM-00465	trained
SA163342	NYSM-00467	trained
SA163343	NYSM-00468	trained
SA163344	NYSM-00474	trained
SA163345	NYSM-00464	trained
SA163346	NYSM-00485	trained
SA163347	NYSM-00473	trained
SA163348	NYSM-00490	trained
SA163349	NYSM-00488	trained
SA163350	NYSM-00487	trained
SA163351	NYSM-00486	trained
SA163352	NYSM-00491	trained

Showing results 1 to 52 of 52

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.

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.

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	ESI
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)
Column Temperature:	40
Solvent A:	5% water/95% methanol; 6.5 mM ammonium bicarbonate, pH 8
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)
Solvent A:	15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, pH 10.8
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:	ESI
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