Summary of Study ST001725

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 PR001105. The data can be accessed directly via it's Project DOI: 10.21228/M8VT4F 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 IDST001725
Study TitleLipidomics dataset of Danio rerio optic nerve regeneration model
Study SummaryThe right optic nerve of 1 year old female and male Danio rerio were crushed and collected three days after. Matching controls of uninjured eyes were also collected. The tissue was dissected from euthanized fish and “flash” frozen on dry ice in Eppendorf tubes. Due to the small size of the nerves, for each category (female crush, female control, male crush, male control) n=24 the samples were pooled. The brain from one male fish was also collected for control/calibration. Lipid extraction was done with the Bligh and Dyer [2] method, followed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) lipid profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. The lipids were identified and quantified with LipidSearch 4.2.21 and the statistical analysis was conducted through Metaboanalyst 5.0.
Institute
University of Miami
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Emailsbhattacharya@med.miami.edu
Phone13054824103
Submit Date2021-03-12
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2021-03-31
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya
https://dx.doi.org/10.21228/M8VT4F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001105
Project DOI:doi: 10.21228/M8VT4F
Project Title:Lipidomics dataset of Danio rerio optic nerve regeneration model
Project Summary:The right optic nerve of 1 year old female and male Danio rerio were crushed and collected three days after. Matching controls of uninjured eyes were also collected. The tissue was dissected from euthanized fish and “flash” frozen on dry ice in Eppendorf tubes. Due to the small size of the nerves, for each category (female crush, female control, male crush, male control) n=24 the samples were pooled. The brain from one male fish was also collected for control/calibration. Lipid extraction was done with the Bligh and Dyer [2] method, followed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) lipid profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. The lipids were identified and quantified with LipidSearch 4.2.21 and the statistical analysis was conducted through Metaboanalyst 5.0.
Institute:University of Miami
Last Name:Bhattacharya
First Name:Sanjoy
Address:1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Email:sbhattacharya@med.miami.edu
Phone:3054824103

Subject:

Subject ID:SU001802
Subject Type:Fish
Subject Species:Danio rerio
Taxonomy ID:7955
Age Or Age Range:1 year old
Gender:Male and female

Factors:

Subject type: Fish; Subject species: Danio rerio (Factor headings shown in green)

mb_sample_id local_sample_id Sample Source
SA162368Brain_02Brain
SA162369Brain_01Brain
SA162370Brain_04Brain
SA162371Brain_03Brain
SA162372Male_Control_04Control
SA162373Female_Control_01Control
SA162374Female_Control_04Control
SA162375Female_Control_03Control
SA162376Female_Control_02Control
SA162377Male_Control_03Control
SA162378Male_Control_02Control
SA162379Male_Control_01Control
SA162380Female_Crush_03Crush
SA162381Male_Crush_01Crush
SA162382Female_Crush_02Crush
SA162383Female_Crush_04Crush
SA162384Male_Crush_02Crush
SA162385Male_Crush_04Crush
SA162386Male_Crush_03Crush
SA162387Female_Crush_01Crush
Showing results 1 to 20 of 20

Collection:

Collection ID:CO001795
Collection Summary:The right optic nerve was crushed in anesthetized, 1 yr old, wildtype fish. The fish recovered from anesthesia in fresh water and placed back into the aquarium system for 3 days. On the third day tissue was dissected from euthanized fish and “flash” frozen on dry ice in Eppendorf tubes. Samples were harvested and frozen within 10 minutes.
Sample Type:Eye tissue

Treatment:

Treatment ID:TR001815
Treatment Summary:No treatment

Sample Preparation:

Sampleprep ID:SP001808
Sampleprep Summary:Lipid extraction was done with the Bligh and Dyer method, followed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) lipid profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system

Combined analysis:

Analysis ID AN002810
Analysis type MS
Chromatography type Reversed phase
Chromatography system Vanquish Horizon Binary UHPLC
Column Accucore Vanquish C18+ UHPLC (50 x 2.1mm,1.5um)
MS Type ESI
MS instrument type Orbitrap
MS instrument name Thermo Q Exactive Orbitrap
Ion Mode UNSPECIFIED
Units ug/ml

Chromatography:

Chromatography ID:CH002076
Instrument Name:Vanquish Horizon Binary UHPLC
Column Name:Accucore Vanquish C18+ UHPLC (50 x 2.1mm,1.5um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002605
Analysis ID:AN002810
Instrument Name:Thermo Q Exactive Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:The lipids were identified and quantified with LipidSearch 4.2.21 and the statistical analysis was conducted through Metaboanalyst 5.0
Ion Mode:UNSPECIFIED
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