Summary of Study ST002776

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 IDST002776
Study TitleZebrafish Optic Nerve Regeneration, Tectum Metabolomics - 3 Days Post Crush
Study SummaryOptic nerve crush provides insight into the metabolome of the tectum. Regenerative model organisms provide key information regarding treatment degeneration in mammalian species; specifically, Zebrafish (Danio Rerio) have the capacity for successful adult optic nerve regeneration. Mammals, however, lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma, diabetes and other optic neuropathies. Optic nerve regeneration as well as the tectum metabolome are often studied to enhance regenerative research. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tectum tissue metabolomic changes in active zebrafish 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 the tecta were collected three days after. Contralateral, uninjured optic nerve tecta 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 = 10-12 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 Date2023-06-29
Num Groups2
Total Subjects67
Num Males36
Num Females31
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-08-07
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 Sex Treatment
SA295652Left_Tectum_2_NEGFemale Injured
SA295653Left_Tectum_1_NEGFemale Injured
SA295654Left_Tectum_3_POSFemale Injured
SA295655Left_Tectum_3_NEGFemale Injured
SA295656Left_Tectum_1_POSFemale Injured
SA295657Left_Tectum_2_POSFemale Injured
SA295658Right_Tectum_3_NEGFemale Uninjured
SA295659Right_Tectum_2_NEGFemale Uninjured
SA295660Right_Tectum_1_POSFemale Uninjured
SA295661Right_Tectum_1_NEGFemale Uninjured
SA295662Right_Tectum_2_POSFemale Uninjured
SA295663Right_Tectum_3_POSFemale Uninjured
SA295664Left_Tectum_5_POSMale Injured
SA295665Left_Tectum_4_NEGMale Injured
SA295666Left_Tectum_6_POSMale Injured
SA295667Left_Tectum_6_NEGMale Injured
SA295668Left_Tectum_5_NEGMale Injured
SA295669Left_Tectum_4_POSMale Injured
SA295670Right_Tectum_6_NEGMale Uninjured
SA295671Right_Tectum_6_POSMale Uninjured
SA295672Right_Tectum_4_NEGMale Uninjured
SA295673Right_Tectum_5_POSMale Uninjured
SA295674Right_Tectum_4_POSMale Uninjured
SA295675Right_Tectum_5_NEGMale Uninjured
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