Summary of Study ST001022

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000683. The data can be accessed directly via it's Project DOI: 10.21228/M8D11B This work is supported by NIH grant, U2C- DK119886.


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 IDST001022
Study TitleCharacterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Brain Tissue (part-III)
Study SummaryCharacterize the metabolomics profile changes during progression of the transition from traumatic brain injury (TBI) to post-traumatic epilepsy (PTE). To do so, three experiments will be performed. PTE animal model will be developed using ferrous chloride injections. Metabolomics profile changes will be obtained before TBI, after TBI, and after PTE development These temporal changes in metabolomics profile during the course of PTE development will be collected. We will also collect cerebrospinal fluid (CSF) at each time point. In addition, we will collect the brain tissue from the center of injury, around the injury, and from the non-injured area for mass spectrometry. In this study, the rat brain tissue at end of study is analyzed.
Mayo Clinic
Last NameSu-youne
First NameChang
Address200 1st Street SW Rochester, MN 55905, USA
Submit Date2018-07-17
Analysis Type DetailLC-MS
Release Date2020-07-15
Release Version1
Chang Su-youne Chang Su-youne application/zip

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Project ID:PR000683
Project DOI:doi: 10.21228/M8D11B
Project Title:Mayo Pilot and Feasibility: Characterization of metabolomics profile changes during development of post-traumatic epilepsy
Project Summary:According to the report from the Centers for Disease Control and Prevention in 2014, traumatic brain injury (TBI) accounts for 30% of all injury-related deaths in the U.S. Developing epilepsy after severe head injury is as high as 40%-50% in some settings. Importantly, many TBI victims develop epilepsy months or years following the initial injury. However, it has not been fully identified how to predict who will develop epilepsy and/or the underlying mechanism of post traumatic epilesy (PTE) development. The main goal of this proposal is to identify the metabolomics biomarker of TBI-induced epilepsy and to investigate the underlying mechanism of the transition from TBI to PTE. To do so, we will develop PTE using two TBI animal models: ferrous chloride injection model and cortical undercut model. Once the brain damage is made, electroencephalogram (EEG) and video monitoring will be performed to determine the onset point of epilepsy. Then, metabolomics profile changes will be analyzed and compared before and after PTE development.
Institute:Mayo Clinic
Last Name:Su-youne
First Name:Chang
Address:200 1st Street SW Rochester, MN 55905, USA


Subject ID:SU001061
Subject Type:Mammal
Subject Species:Rattus norvegicus
Taxonomy ID:10116


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

mb_sample_id local_sample_id Groups Tissues
SA064156nC18-07sep17-001C Cortex
SA064157nhilic-07sep17-002C Cortex
SA064158pC18-09sep17-004C Cortex
SA064159pC18-09sep17-003C Cortex
SA064160pC18-05sep17-002C Cortex
SA064161nhilic-09sep17-003C Cortex
SA064162nhilic-09sep17-004C Cortex
SA064163philic-08sep17-004C Cortex
SA064164philic-08sep17-003C Cortex
SA064165philic-06sep17-002C Cortex
SA064166philic-06sep17-001C Cortex
SA064167pC18-05sep17-001C Cortex
SA064168nhilic-07sep17-001C Cortex
SA064169nC18-11sep17-004C Cortex
SA064170nC18-07sep17-002C Cortex
SA064171nC18-11sep17-003C Cortex
SA064172philic-08sep17-016C Hippocampus
SA064173nC18-11sep17-016C Hippocampus
SA064174pC18-05sep17-013C Hippocampus
SA064175nhilic-09sep17-016C Hippocampus
SA064176pC18-05sep17-014C Hippocampus
SA064177pC18-09sep17-016C Hippocampus
SA064178philic-06sep17-013C Hippocampus
SA064179philic-06sep17-014C Hippocampus
SA064180nC18-11sep17-015C Hippocampus
SA064181nhilic-07sep17-014C Hippocampus
SA064182nhilic-09sep17-015C Hippocampus
SA064183nhilic-07sep17-013C Hippocampus
SA064184philic-08sep17-015C Hippocampus
SA064185nC18-07sep17-014C Hippocampus
SA064186nC18-07sep17-013C Hippocampus
SA064187pC18-09sep17-015C Hippocampus
SA064212pC18-09sep17-031F_inj Cortex
SA064213pC18-05sep17-030F_inj Cortex
SA064214philic-06sep17-030F_inj Cortex
SA064215pC18-05sep17-029F_inj Cortex
SA064216nhilic-09sep17-031F_inj Cortex
SA064217nhilic-07sep17-030F_inj Cortex
SA064218philic-08sep17-031F_inj Cortex
SA064219nhilic-07sep17-029F_inj Cortex
SA064220nC18-07sep17-029F_inj Cortex
SA064221nC18-07sep17-030F_inj Cortex
SA064222nC18-11sep17-031F_inj Cortex
SA064223philic-06sep17-029F_inj Cortex
SA064224philic-06sep17-037F_inj Hippocampus
SA064225nhilic-07sep17-037F_inj Hippocampus
SA064226nhilic-07sep17-038F_inj Hippocampus
SA064227philic-08sep17-039F_inj Hippocampus
SA064228nC18-11sep17-039F_inj Hippocampus
SA064229nC18-07sep17-038F_inj Hippocampus
SA064230nC18-07sep17-037F_inj Hippocampus
SA064231pC18-09sep17-039F_inj Hippocampus
SA064232philic-06sep17-038F_inj Hippocampus
SA064233nhilic-09sep17-039F_inj Hippocampus
SA064234pC18-05sep17-038F_inj Hippocampus
SA064235pC18-05sep17-037F_inj Hippocampus
SA064188pC18-05sep17-009F Cortex
SA064189pC18-09sep17-011F Cortex
SA064190pC18-05sep17-010F Cortex
SA064191philic-06sep17-009F Cortex
SA064192nhilic-07sep17-010F Cortex
SA064193nhilic-09sep17-011F Cortex
SA064194nhilic-07sep17-009F Cortex
SA064195nC18-07sep17-009F Cortex
SA064196nC18-07sep17-010F Cortex
SA064197philic-06sep17-010F Cortex
SA064198philic-08sep17-011F Cortex
SA064199nC18-11sep17-011F Cortex
SA064200nC18-11sep17-023F Hippocampus
SA064201nC18-07sep17-022F Hippocampus
SA064202philic-06sep17-021F Hippocampus
SA064203pC18-05sep17-022F Hippocampus
SA064204pC18-09sep17-023F Hippocampus
SA064205philic-08sep17-023F Hippocampus
SA064206pC18-05sep17-021F Hippocampus
SA064207nC18-07sep17-021F Hippocampus
SA064208nhilic-09sep17-023F Hippocampus
SA064209nhilic-07sep17-021F Hippocampus
SA064210philic-06sep17-022F Hippocampus
SA064211nhilic-07sep17-022F Hippocampus
SA064244pC18-09sep17-032R_inj Cortex
SA064245nC18-11sep17-032R_inj Cortex
SA064246philic-08sep17-032R_inj Cortex
SA064247nhilic-09sep17-032R_inj Cortex
SA064248nC18-11sep17-040R_inj Hippocampus
SA064249nhilic-09sep17-040R_inj Hippocampus
SA064250philic-08sep17-040R_inj Hippocampus
SA064251pC18-09sep17-040R_inj Hippocampus
SA064236nhilic-09sep17-012R Cortex
SA064237pC18-09sep17-012R Cortex
SA064238philic-08sep17-012R Cortex
SA064239nC18-11sep17-012R Cortex
SA064240pC18-09sep17-024R Hippocampus
SA064241philic-08sep17-024R Hippocampus
SA064242nC18-11sep17-024R Hippocampus
SA064243nhilic-09sep17-024R Hippocampus
SA064284philic-08sep17-028S_inj Cortex
SA064285philic-08sep17-027S_inj Cortex
SA064286philic-06sep17-025S_inj Cortex
SA064287nC18-07sep17-026S_inj Cortex
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Collection ID:CO001055
Collection Summary:Rats will either be controls, injected with saline, or injected with ferrous chloride to influence PTE. Also one of the ferrous chloride treated rats was repeated (R_no_cx, R_no_hp, R_inj_cx, R_inj_hp). Study Groupings: C_no_cx = control, no injections, cortex tissue C_no_hp = control, no injections, hippocampus tissue S_no_cx = saline treated, cortex tissue not near injection site S_no_hp = saline treated, hippocampus tissue not near injection site S_inj_cx = saline treated, cortex tissue at injection site S_inj_hp = saline treated, hippocampus tissue at injection site F_no_cx = ferrous chloride treated, cortex tissue not near injection site F_no_hp = ferrou chloride treated, hippocampus tissue not near injection site F_inj_cx = ferrous chloride treated, cortex tissue at injection site F_inj_hp = ferrous chloride treated, hippocampus tissue at injection site Experimental Flow Day0: baseline pre TBI. Blood and CSF collected Day1: Surgery for TBI. Injections of Ferrous Cloride or Saline Day2: CSF collected Weeks1-3: montoring to determine PTE starting point. Blood and CSF collected 1 Month: montoring of PTE. Blood and CSF collected 2 Month: Animal is euthanized and blood, CSF, and tissue harvested
Sample Type:Brain


Treatment ID:TR001075
Treatment Summary:Rats will either be controls, injected with saline, or injected with ferrous chloride to influence PTE. Trauma-Induced Epilepsy Model: Ferrous chloride injection model: Ferrous chloride solution (5 μl of 100 mM with saline) will be injected at a rate of 0.5 μl/min through a Hamilton micro-syringe controlled by a micro-pump (UMP3, WPI, FL). Once the ferrous chloride solution injection is completed, the syringe will remain in position for 5 minutes, and then it will be removed slowly. The burr holes will be closed with light-curing dental cement. The dose of ferrous chloride injection was determined from prior published reports from mouse, rat, and cat. They all used 100 mM ferrous chloride aqueous solution and volumes were various: 1 μl for mouse,14 5 μl for rat (200-300 g),15 and 10 μl for cat (2-4 Kg).15 Video monitoring: The use of 24 x 7 video monitoring and review means that we do not have to rely on the rats having seizures during daily rounding or at some other time when a human happens to be present in the home cage. Normally, the video will be watched in time lapse, fast-forward mode to scan for potential seizures. The reviewer can then stop the video, rewind and watch the behavioral episode in real-time or slow motion to determine whether a seizure actually occurred. Behavioral seizures will be identified by any combination or sequence of the following: loss of postural control (opisthotonus), tonic flexion or extension of limbs or head/neck, and clonic movements of limbs or head/neck. Often, behavioral seizures in rats may be accompanied by drooling, urination and facial twitches, although these may not always be observable on video. In addition, seizures will likely be followed by a postictal phase, which may include a period of running, jumping and general agitation. Video monitoring cannot detect subclinical or electrographic seizures (i.e., seizures without a behavioral component). Video will be reviewed in this way for each rat in order to establish that a cortical injured rat does indeed have epilepsy, to establish the “typical seizure” pattern in each rat, and to help establish a seizure frequency baseline, although it is understood that video monitoring alone might occasionally miss a seizure. EEG monitoring: To prevent imaging distortion and ferromagnetic interference, graphite carbon electrodes will be fabricated and/or purchased. A total of five electrodes will be implanted for EEG monitoring on the skull. EEG will be monitored with the Open EPhys System.18 While EEG recording, EEG electrodes will be connected to wires attached to the ceiling of a cage. In trauma-induced epilepsy rats, spontaneous neural activity will be recorded using a wide bandwidth (0-9 kHz) recording system. Post-analysis will be used to identify epilepsy signals.

Sample Preparation:

Sampleprep ID:SP001068
Sampleprep Summary:large scale profiling of rat cortex and hippocampus brian tissue. The brain tissue and CSF will be collected for mass spectrometry. To prepare samples, proteins will be removed from collected dialysates by adding cold methanol:water (8:1, v/v) mixture containing 5.0 μg internal standard (IS), myristic-d27 acid, at ambient temperature. Samples will be vortexed for 1 min, incubated on ice for 15 min, and then centrifuged. The supernatant will be completely dried in a SpeedVac, and the lyophilized sample will be subsequently methoxiaminated using 20 μl of a 20 mg/ml solution of methoxyamine hydrochloride in pyridine at 30°C for 90 min and derivatized using 80 μL of N-methyl-N-trimethylsilyltrifluoroacetamide with 1% trimethylchloro-silane (MSTFA + 1% TMCS, Pierce) at 37°C for 30 min.

Combined analysis:

Analysis ID AN001676 AN001677 AN001678 AN001679
Analysis type MS MS MS MS
Chromatography type HILIC HILIC Reversed phase Reversed phase
Chromatography system Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity Agilent 1290 Infinity
Column Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity BEH Amide (150 x 2.1mm,1.7um) Waters Acquity HSS C18 (150 x 2.1mm,1.8um) Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
MS instrument type QTOF QTOF QTOF QTOF
MS instrument name Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF Agilent 6550 QTOF
Units intensity intensity intensity intensity


Chromatography ID:CH001179
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity BEH Amide (150 x 2.1mm,1.7um)
Chromatography Type:HILIC
Chromatography ID:CH001180
Instrument Name:Agilent 1290 Infinity
Column Name:Waters Acquity HSS C18 (150 x 2.1mm,1.8um)
Chromatography Type:Reversed phase


MS ID:MS001551
Analysis ID:AN001676
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS ID:MS001552
Analysis ID:AN001677
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS ID:MS001553
Analysis ID:AN001678
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF
MS ID:MS001554
Analysis ID:AN001679
Instrument Name:Agilent 6550 QTOF
Instrument Type:QTOF