Summary of Study ST001022
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 PR000683. The data can be accessed directly via it's Project DOI: 10.21228/M8D11B 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 | ST001022 |
| Study Title | Characterization of metabolomics profile changes during development of post-traumatic epilepsy in Rat Brain Tissue (part-III) |
| Study Summary | Characterize 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. |
| Institute | Mayo Clinic |
| Last Name | Su-youne |
| First Name | Chang |
| Address | 200 1st Street SW Rochester, MN 55905, USA |
| Chang.SuYoune@mayo.edu | |
| Phone | 1-507-293-0511 |
| Submit Date | 2018-07-17 |
| Analysis Type Detail | LC-MS |
| Release Date | 2020-07-15 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| 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 |
| Email: | Chang.SuYoune@mayo.edu |
| Phone: | 1-507-293-0511 |
Subject:
| Subject ID: | SU001061 |
| Subject Type: | Mammal |
| Subject Species: | Rattus norvegicus |
| Taxonomy ID: | 10116 |
Factors:
Subject type: Mammal; Subject species: Rattus norvegicus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Groups | Tissues |
|---|---|---|---|
| SA064156 | nC18-07sep17-001 | C | Cortex |
| SA064157 | nhilic-07sep17-002 | C | Cortex |
| SA064158 | pC18-09sep17-004 | C | Cortex |
| SA064159 | pC18-09sep17-003 | C | Cortex |
| SA064160 | pC18-05sep17-002 | C | Cortex |
| SA064161 | nhilic-09sep17-003 | C | Cortex |
| SA064162 | nhilic-09sep17-004 | C | Cortex |
| SA064163 | philic-08sep17-004 | C | Cortex |
| SA064164 | philic-08sep17-003 | C | Cortex |
| SA064165 | philic-06sep17-002 | C | Cortex |
| SA064166 | philic-06sep17-001 | C | Cortex |
| SA064167 | pC18-05sep17-001 | C | Cortex |
| SA064168 | nhilic-07sep17-001 | C | Cortex |
| SA064169 | nC18-11sep17-004 | C | Cortex |
| SA064170 | nC18-07sep17-002 | C | Cortex |
| SA064171 | nC18-11sep17-003 | C | Cortex |
| SA064172 | philic-08sep17-016 | C | Hippocampus |
| SA064173 | nC18-11sep17-016 | C | Hippocampus |
| SA064174 | pC18-05sep17-013 | C | Hippocampus |
| SA064175 | nhilic-09sep17-016 | C | Hippocampus |
| SA064176 | pC18-05sep17-014 | C | Hippocampus |
| SA064177 | pC18-09sep17-016 | C | Hippocampus |
| SA064178 | philic-06sep17-013 | C | Hippocampus |
| SA064179 | philic-06sep17-014 | C | Hippocampus |
| SA064180 | nC18-11sep17-015 | C | Hippocampus |
| SA064181 | nhilic-07sep17-014 | C | Hippocampus |
| SA064182 | nhilic-09sep17-015 | C | Hippocampus |
| SA064183 | nhilic-07sep17-013 | C | Hippocampus |
| SA064184 | philic-08sep17-015 | C | Hippocampus |
| SA064185 | nC18-07sep17-014 | C | Hippocampus |
| SA064186 | nC18-07sep17-013 | C | Hippocampus |
| SA064187 | pC18-09sep17-015 | C | Hippocampus |
| SA064212 | pC18-09sep17-031 | F_inj | Cortex |
| SA064213 | pC18-05sep17-030 | F_inj | Cortex |
| SA064214 | philic-06sep17-030 | F_inj | Cortex |
| SA064215 | pC18-05sep17-029 | F_inj | Cortex |
| SA064216 | nhilic-09sep17-031 | F_inj | Cortex |
| SA064217 | nhilic-07sep17-030 | F_inj | Cortex |
| SA064218 | philic-08sep17-031 | F_inj | Cortex |
| SA064219 | nhilic-07sep17-029 | F_inj | Cortex |
| SA064220 | nC18-07sep17-029 | F_inj | Cortex |
| SA064221 | nC18-07sep17-030 | F_inj | Cortex |
| SA064222 | nC18-11sep17-031 | F_inj | Cortex |
| SA064223 | philic-06sep17-029 | F_inj | Cortex |
| SA064224 | philic-06sep17-037 | F_inj | Hippocampus |
| SA064225 | nhilic-07sep17-037 | F_inj | Hippocampus |
| SA064226 | nhilic-07sep17-038 | F_inj | Hippocampus |
| SA064227 | philic-08sep17-039 | F_inj | Hippocampus |
| SA064228 | nC18-11sep17-039 | F_inj | Hippocampus |
| SA064229 | nC18-07sep17-038 | F_inj | Hippocampus |
| SA064230 | nC18-07sep17-037 | F_inj | Hippocampus |
| SA064231 | pC18-09sep17-039 | F_inj | Hippocampus |
| SA064232 | philic-06sep17-038 | F_inj | Hippocampus |
| SA064233 | nhilic-09sep17-039 | F_inj | Hippocampus |
| SA064234 | pC18-05sep17-038 | F_inj | Hippocampus |
| SA064235 | pC18-05sep17-037 | F_inj | Hippocampus |
| SA064188 | pC18-05sep17-009 | F | Cortex |
| SA064189 | pC18-09sep17-011 | F | Cortex |
| SA064190 | pC18-05sep17-010 | F | Cortex |
| SA064191 | philic-06sep17-009 | F | Cortex |
| SA064192 | nhilic-07sep17-010 | F | Cortex |
| SA064193 | nhilic-09sep17-011 | F | Cortex |
| SA064194 | nhilic-07sep17-009 | F | Cortex |
| SA064195 | nC18-07sep17-009 | F | Cortex |
| SA064196 | nC18-07sep17-010 | F | Cortex |
| SA064197 | philic-06sep17-010 | F | Cortex |
| SA064198 | philic-08sep17-011 | F | Cortex |
| SA064199 | nC18-11sep17-011 | F | Cortex |
| SA064200 | nC18-11sep17-023 | F | Hippocampus |
| SA064201 | nC18-07sep17-022 | F | Hippocampus |
| SA064202 | philic-06sep17-021 | F | Hippocampus |
| SA064203 | pC18-05sep17-022 | F | Hippocampus |
| SA064204 | pC18-09sep17-023 | F | Hippocampus |
| SA064205 | philic-08sep17-023 | F | Hippocampus |
| SA064206 | pC18-05sep17-021 | F | Hippocampus |
| SA064207 | nC18-07sep17-021 | F | Hippocampus |
| SA064208 | nhilic-09sep17-023 | F | Hippocampus |
| SA064209 | nhilic-07sep17-021 | F | Hippocampus |
| SA064210 | philic-06sep17-022 | F | Hippocampus |
| SA064211 | nhilic-07sep17-022 | F | Hippocampus |
| SA064244 | pC18-09sep17-032 | R_inj | Cortex |
| SA064245 | nC18-11sep17-032 | R_inj | Cortex |
| SA064246 | philic-08sep17-032 | R_inj | Cortex |
| SA064247 | nhilic-09sep17-032 | R_inj | Cortex |
| SA064248 | nC18-11sep17-040 | R_inj | Hippocampus |
| SA064249 | nhilic-09sep17-040 | R_inj | Hippocampus |
| SA064250 | philic-08sep17-040 | R_inj | Hippocampus |
| SA064251 | pC18-09sep17-040 | R_inj | Hippocampus |
| SA064236 | nhilic-09sep17-012 | R | Cortex |
| SA064237 | pC18-09sep17-012 | R | Cortex |
| SA064238 | philic-08sep17-012 | R | Cortex |
| SA064239 | nC18-11sep17-012 | R | Cortex |
| SA064240 | pC18-09sep17-024 | R | Hippocampus |
| SA064241 | philic-08sep17-024 | R | Hippocampus |
| SA064242 | nC18-11sep17-024 | R | Hippocampus |
| SA064243 | nhilic-09sep17-024 | R | Hippocampus |
| SA064284 | philic-08sep17-028 | S_inj | Cortex |
| SA064285 | philic-08sep17-027 | S_inj | Cortex |
| SA064286 | philic-06sep17-025 | S_inj | Cortex |
| SA064287 | nC18-07sep17-026 | S_inj | Cortex |
Collection:
| 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:
| 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 Type | ESI | ESI | ESI | ESI |
| MS instrument type | QTOF | QTOF | QTOF | QTOF |
| MS instrument name | Agilent 6550 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF | Agilent 6550 QTOF |
| Ion Mode | POSITIVE | NEGATIVE | POSITIVE | NEGATIVE |
| Units | intensity | intensity | intensity | intensity |
Chromatography:
| 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:
| MS ID: | MS001551 |
| Analysis ID: | AN001676 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001552 |
| Analysis ID: | AN001677 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| MS ID: | MS001553 |
| Analysis ID: | AN001678 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| MS ID: | MS001554 |
| Analysis ID: | AN001679 |
| Instrument Name: | Agilent 6550 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
