Summary of Study ST002444

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 PR001575. The data can be accessed directly via it's Project DOI: 10.21228/M83X51 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 IDST002444
Study TitleZebrafish Optic Nerve Regeneration Metabolomics - 3 Days Post Crush
Study SummaryZebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. In contrast, mammals lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma and other optic neuropathies. Optic nerve regeneration is often studied using optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish optic nerve regeneration can elucidate prioritized metabolite pathways that can be targeted in mammalian systems for therapeutic development. Female and male (6 month to 1 year old) right Zebrafish (Tg(gap43:GFP)) optic nerves were crushed and collected three days after. Contralateral, uninjured optic nerves were collected as controls. The tissue was dissected from euthanized fish and frozen on dry ice. Samples were pooled for each category (female crush, female control, male crush, male control) and pooled at n = 31 to obtain sufficient metabolite concentrations for analysis. Optic nerve regeneration was verified by microscope visualization of GFP fluorescence. Metabolites were extracted using a Precellys Homogenizer and a serial extraction method: (1) 1:1 Methanol/Water and (2) 8:1:1 Acetonitrile/Methanol/Acetone. Metabolites were analyzed by untargeted liquid chromatography-mass spectrometry (LC MS-MS) profiling using a Q-Exactive Orbitrap instrument coupled with Vanquish Horizon Binary UHPLC LC-MS system. Metabolites were identified and quantified using Compound Discoverer 3.3 and isotopic internal metabolites standards.
University of Miami
DepartmentMcKnight - Ophthalmology
LaboratoryBhattacharya Lab
Last NameBhattacharya
First NameSanjoy
Address1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Submit Date2022-12-19
Num Groups2
Total Subjects67
Num Males36
Num Females31
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2023-01-25
Release Version1
Sanjoy Bhattacharya Sanjoy Bhattacharya application/zip

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

mb_sample_id local_sample_id Gender Treatment
SA244574Right_Optic_Nerve_1_2_POSFemale Injured
SA244575Right_Optic_Nerve_1_3_NEGFemale Injured
SA244576Right_Optic_Nerve_1_1_POSFemale Injured
SA244577Right_Optic_Nerve_1_3_POSFemale Injured
SA244578Right_Optic_Nerve_1_1_NEGFemale Injured
SA244579Right_Optic_Nerve_1_2_NEGFemale Injured
SA244580Left_Optic_Nerve_1_2_NEGFemale Uninjured
SA244581Left_Optic_Nerve_1_3_NEGFemale Uninjured
SA244582Left_Optic_Nerve_1_1_NEGFemale Uninjured
SA244583Left_Optic_Nerve_1_3_POSFemale Uninjured
SA244584Left_Optic_Nerve_1_2_POSFemale Uninjured
SA244585Left_Optic_Nerve_1_1_POSFemale Uninjured
SA244586Right_Optic_Nerve_2_2_NEGMale Injured
SA244587Right_Optic_Nerve_2_3_NEGMale Injured
SA244588Right_Optic_Nerve_2_1_NEGMale Injured
SA244589Right_Optic_Nerve_2_3_POSMale Injured
SA244590Right_Optic_Nerve_2_2_POSMale Injured
SA244591Right_Optic_Nerve_2_1_POSMale Injured
SA244592Left_Optic_Nerve_2_3_NEGMale Uninjured
SA244593Left_Optic_Nerve_2_2_POSMale Uninjured
SA244594Left_Optic_Nerve_2_1_POSMale Uninjured
SA244595Left_Optic_Nerve_2_3_POS_20221118115945Male Uninjured
SA244596Left_Optic_Nerve_2_2_NEGMale Uninjured
SA244597Left_Optic_Nerve_2_1_NEGMale Uninjured
SA244598System_Suitability_Blank_NEG_20221119033833N/A N/A
SA244599Pooled_QC2_ON_NEGN/A N/A
SA244600Pooled_QC_MS2_2_ON_NEGN/A N/A
SA244601System_Suitability_Blank_NEGN/A N/A
SA244602Pooled_QC_MS2_1_ON_POSN/A N/A
SA244603Pooled_QC2_ON_POSN/A N/A
SA244604Pooled_QC1_ON_POSN/A N/A
SA244605System_Suitability_Blank_POS_20221118022039N/A N/A
SA244606Extraction_Blank_1_POSN/A N/A
SA244607Pooled_QC_MS2_2_ON_POSN/A N/A
SA244608System_Suitability_Blank_POS_20221118065605N/A N/A
SA244609System_Suitability_Blank_NEG_20221118230351N/A N/A
SA244610Pooled_QC1_ON_NEGN/A N/A
SA244611System_Suitability_Blank_NEG_20221118182825N/A N/A
SA244612Extraction_Blank_1_NEGN/A N/A
SA244613System_Suitability_Blank_POSN/A N/A
SA244614Pooled_QC_MS2_1_ON_NEGN/A N/A
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