Summary of study ST001273

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 PR000859. The data can be accessed directly via it's Project DOI: 10.21228/M8NH5V 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 IDST001273
Study TitleLipidomics Dataset of Sonication-Induced Traumatic Optic Neuropathy in Mice
Study SummaryTraumatic optic neuropathy (TON) is the loss of vision secondary to trauma. Approximately two weeks after traumatic damage, diffuse retinal ganglion cell loss and axon degeneration of the optic nerve are exhibited. Here we present the changes that occur in the optic nerve lipidome of two-month-old C57BL/6J mice following sonication-induced TON (SI-TON), which closely models the indirect clinical mechanism in TON. Optic nerves were harvested at three time points following injury: 1-day, 7-days, and 14-days for comparison with the control group (uninjured optic nerves from 2-month-old mice). Lipidomic changes were observed at each of the various time points, with a pattern of progression present in multiple lipid classes. This data demonstrates the distinct lipidomic changes at each time point following indirect trauma to the optic nerve.
Institute
University of Miami
DepartmentOphthalmology, Bascom Palmer Eye Institute
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Suite 707A University of Miami Miami, FL, 33136
EmailSBhattacharya@med.miami.edu
Phone305-482-4103
Submit Date2019-06-10
Num Groups4
Total Subjects31
Num Males15
Num Females16
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2019-11-20
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M8NH5V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000859
Project DOI:doi: 10.21228/M8NH5V
Project Title:Lipidomics Dataset of Sonication-Induced Traumatic Optic Neuropathy in Mice
Project Summary:Traumatic optic neuropathy (TON) is the loss of vision secondary to trauma. Approximately two weeks after traumatic damage, diffuse retinal ganglion cell loss and axon degeneration of the optic nerve are exhibited. Here we presented the changes that occured in the optic nerve lipidome of two-month-old C57BL/6J mice following sonication-induced TON Optic nerves were harvested at three time points following injury: 1-day, 7-days, and 14-days for comparison with the control group (uninjured optic nerves from 2-month-old mice). Lipidomic changes were observed at each of the various time points, with a pattern of progression present in multiple lipid classes.
Institute:University of Miami
Department:Ophthalmology, Bascom Palmer Eye Institute
Last Name:Bhattacharya
First Name:Sanjoy
Address:1638 NW 10th Avenue, Suite 707A University of Miami Miami, FL, 33136
Email:SBhattacharya@med.miami.edu
Phone:305-482-4103

Subject:

Subject ID:SU001345
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:C57BL/6J
Age Or Age Range:2 Months
Gender:Male and female

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Exposure Days Post Exposure
SA092997C7-No Sonication Control
SA092998C6-No Sonication Control
SA092999C6+No Sonication Control
SA093000C8+No Sonication Control
SA093001C8-No Sonication Control
SA093002C1+No Sonication Control
SA093003C1-No Sonication Control
SA093004C5-No Sonication Control
SA093005C7+No Sonication Control
SA093006C3+No Sonication Control
SA093007C5+No Sonication Control
SA093008C2+No Sonication Control
SA093009C3-No Sonication Control
SA093010C2-No Sonication Control
SA093011C4+No Sonication Control
SA093012C4-No Sonication Control
SA093013D14_3-Sonication Day Fourteen
SA093014D14_4+Sonication Day Fourteen
SA093015D14_3+Sonication Day Fourteen
SA093016D14_2+Sonication Day Fourteen
SA093017D14_4-Sonication Day Fourteen
SA093018D14_1-Sonication Day Fourteen
SA093019D14_2-Sonication Day Fourteen
SA093020D14_1+Sonication Day Fourteen
SA093021D14_7-Sonication Day Fourteen
SA093022D14_8+Sonication Day Fourteen
SA093023D14_8-Sonication Day Fourteen
SA093024D14_7+Sonication Day Fourteen
SA093025D14_6-Sonication Day Fourteen
SA093026D14_5-Sonication Day Fourteen
SA093027D14_6+Sonication Day Fourteen
SA093028D14_5+Sonication Day Fourteen
SA093029D1_8-Sonication Day One
SA093030D1_5+Sonication Day One
SA093031D1_4-Sonication Day One
SA093032D1_5-Sonication Day One
SA093033D1_6+Sonication Day One
SA093034D1_7+Sonication Day One
SA093035D1_6-Sonication Day One
SA093036D1_4+Sonication Day One
SA093037D1_3-Sonication Day One
SA093038D1_1-Sonication Day One
SA093039D1_1+Sonication Day One
SA093040D1_2+Sonication Day One
SA093041D1_2-Sonication Day One
SA093042D1_3+Sonication Day One
SA093043D1_7-Sonication Day One
SA093044D1_8+Sonication Day One
SA093045D7_4-Sonication Day Seven
SA093046D7_5+Sonication Day Seven
SA093047D7_4+Sonication Day Seven
SA093048D7_3-Sonication Day Seven
SA093049D7_2-Sonication Day Seven
SA093050D7_3+Sonication Day Seven
SA093051D7_5-Sonication Day Seven
SA093052D7_6+Sonication Day Seven
SA093053D7_1-Sonication Day Seven
SA093054D7_1+Sonication Day Seven
SA093055D7_7-Sonication Day Seven
SA093056D7_7+Sonication Day Seven
SA093057D7_6-Sonication Day Seven
SA093058D7_2+Sonication Day Seven
Showing results 1 to 62 of 62

Collection:

Collection ID:CO001339
Collection Summary:Mice were exposed to a controlled sonication pulse and optic nerve samples were collected at 1 day, 7 days, and 14 days post sonication. Lipids were then extracted, resuspended in Chloroform:Methanol (1:1) and processed through untargeted liquid chromatography Q-Exactive Orbitrap tandem mass spectrometry (LC-MS/MS).
Sample Type:optic nerve

Treatment:

Treatment ID:TR001360
Treatment Summary:Mice were exposed to a 500msec sonication shock at the supraorbital rim that did not create any skull fractures nor cause death. Mice were sacrificed at 1 day, 7 days, or 14 days post exposure for lipid analysis of optic nerves.

Sample Preparation:

Sampleprep ID:SP001353
Sampleprep Summary:As described in collection

Combined analysis:

Analysis ID AN002113 AN002114
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Accela 600 Thermo Accela 600
Column Thermo Acclaim C18 (150 x 2.1mm, 3µm) Thermo Acclaim C18 (150 x 2.1mm, 3µm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive Orbitrap Thermo Q Exactive Orbitrap
Ion Mode POSITIVE NEGATIVE
Units Main area Main area

Chromatography:

Chromatography ID:CH001547
Instrument Name:Thermo Accela 600
Column Name:Thermo Acclaim C18 (150 x 2.1mm, 3µm)
Chromatography Type:Reversed phase

MS:

MS ID:MS001968
Analysis ID:AN002113
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:A Heated Electrospray Ionization Source (HESI) was operated at a spray voltage of 4.4kV, a HESI vaporization temperature of 275°C, a sheath gas pressure of 45 arbitrary units, and an auxillary gas flow of 15 arbitrary units. The ion transfer tube was kept at a temperature of 350°C. The scan range was set at 150-1500 m/z.
Ion Mode:POSITIVE
  
MS ID:MS001969
Analysis ID:AN002114
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:A Heated Electrospray Ionization Source (HESI) was operated at a spray voltage of 4.4kV, a HESI vaporization temperature of 275°C, a sheath gas pressure of 45 arbitrary units, and an auxillary gas flow of 15 arbitrary units. The ion transfer tube was kept at a temperature of 350°C. The scan range was set at 150-1500 m/z.
Ion Mode:NEGATIVE
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