Summary of Study ST002775

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 PR001575. The data can be accessed directly via it's Project DOI: 10.21228/M83X51 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	ST002775
Study Title	Zebrafish Retina Regeneration Metabolomics - 3 Days Post Crush
Study Summary	Retinal regeneration has been at the forefront of optic research. Regenerative model organisms provide key information regarding treatment for optic nerve and retinal degeneration in mammalian species; specifically, Zebrafish (Danio Rerio) have the capacity for successful adult retinal regeneration. Mammals, however, lack this intrinsic ability and undergo irreversible neurodegeneration seen in glaucoma, diabetes and other optic neuropathies. Optic nerve and retinal regeneration are often studied using the retina obtained via optic nerve crush, a mechanical neurodegenerative model. Untargeted metabolomic studies within successful regenerative models are deficient. Evaluation of tissue metabolomic changes in active zebrafish retinal 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 retinas were collected three days after. Contralateral, uninjured optic nerve retinas 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. Retinal 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.
Institute	University of Miami
Department	McKnight - Ophthalmology
Laboratory	Bhattacharya Lab
Last Name	Bhattacharya
First Name	Sanjoy
Address	1638 NW 10th Avenue, Room 706-A, Miami, FL 33136
Email	sbhattacharya@med.miami.edu
Phone	3054824103
Submit Date	2023-06-20
Num Groups	2
Total Subjects	67
Num Males	36
Num Females	31
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-08-07
Release Version	1

Select appropriate tab below to view additional metadata details:

Project:

Project ID:	PR001575
Project DOI:	doi: 10.21228/M83X51
Project Title:	Regenerative Metabolomic Profiles of the Zebrafish Visual System
Project Summary:	Zebrafish (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. Currently, 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 to 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. The associated retinas and tecta were also collected under the same conditions for metabolic analysis. Contralateral, uninjured optic nerves, retinas and tecta were collected as controls. The three tissue types (optic nerve, retina, and tectum) were dissected from euthanized fish and frozen on dry ice. Optic nerve 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. Retina and tectum samples were pooled using the same categories (female crush, female control, male crush, male control) at n = 10-12. 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 metabolite standards.
Institute:	University of Miami
Department:	McKnight - Ophthalmology
Laboratory:	Bhattacharya Lab
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:	SU002882
Subject Type:	Fish
Subject Species:	Danio rerio
Taxonomy ID:	7955
Gender:	Male and female

Factors:

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

mb_sample_id	local_sample_id	Sex	Treatment
SA295628	Right_Retina_2_NEG	Female	Injured
SA295629	Right_Retina_3_NEG	Female	Injured
SA295630	Right_Retina_1_POS	Female	Injured
SA295631	Right_Retina_1_NEG	Female	Injured
SA295632	Right_Retina_3_POS	Female	Injured
SA295633	Right_Retina_2_POS	Female	Injured
SA295634	Left_Retina _1_NEG	Female	Uninjured
SA295635	Left_Retina_3_POS	Female	Uninjured
SA295636	Left_Retina_2_NEG	Female	Uninjured
SA295637	Left_Retina _1_POS	Female	Uninjured
SA295638	Left_Retina_3_NEG	Female	Uninjured
SA295639	Left_Retina_2_POS	Female	Uninjured
SA295640	Right_Retina_6_NEG	Male	Injured
SA295641	Right_Retina_4_POS	Male	Injured
SA295642	Right_Retina_5_NEG	Male	Injured
SA295643	Right_Retina_4_NEG	Male	Injured
SA295644	Right_Retina_6_POS	Male	Injured
SA295645	Right_Retina_5_POS	Male	Injured
SA295646	Left_Retina_6_NEG	Male	Uninjured
SA295647	Left_Retina_6_POS	Male	Uninjured
SA295648	Left_Retina_5_POS	Male	Uninjured
SA295649	Left_Retina_5_NEG	Male	Uninjured
SA295650	Left_Retina_4_POS	Male	Uninjured
SA295651	Left_Retina_4_NEG	Male	Uninjured

Showing results 1 to 24 of 24

Showing results 1 to 24 of 24

Collection:

Collection ID:	CO002875
Collection Summary:	In the tissue collection process, mice were euthanized using an overdose of MS-222. The optic nerve was removed via dissection from the optic nerve head to the optic chiasm. The retinas of both female and male Zebrafish were collected and separated into biological samples. Due to the small tissue and metabolomics resolution constraints, optic nerves were pooled to generate higher signal intensities. A total of 10-11 and 12 retinas were pooled from female and male zebrafish samples, respectively. The untreated retinas were pooled using the same protocol.
Sample Type:	Eye tissue

Treatment:

Treatment ID:	TR002891
Treatment Summary:	For optic nerve crush, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5–1 mm from the optic nerve head for 5 s. Success was observed by the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 h the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.

Treatment ID:

TR002891

Treatment Summary:

For optic nerve crush, animals were deeply anesthetized in 0.033% tricaine methane-sulfonate (MS-222). The right optic nerve was exposed by gently removing the connective tissue on the dorsal half of the eye and rotating the eye ventrally out of the orbit with a number 5 forceps. A nerve crush was then performed using number 5 forceps to crush the nerve ~0.5–1 mm from the optic nerve head for 5 s. Success was observed by the generation of a translucent stripe in the nerve that completely separated two areas of white myelination with no bleeding. Fish were then revived in fresh aquatic system water in individual tanks. After 1 h the tanks were returned to the fish system and animals were maintained normally with daily feeding until 3 days post injury.

Sample Preparation:

Sampleprep ID:	SP002888
Sampleprep Summary:	Retinas remained on dry ice to prevent metabolite degradation while the metabolite extraction was conducted. Tissues were transferred to 0.5mL Soft Tissue Lysing Kit Precellys tubes containing beads. Then, 84 µL of chilled 1:1 MeOH/H2O were added to Precellys tube. Pre-extraction internal standards were added to the tubes: 5µl of 1mg/ml Caffeine 13C6, 5µl of 1mg/ml D-Glucose 13C6, 5µl of 1mg/ml Oleic Acid 13C5, and 1µl of 5mg/mL Isoleucine 13C6 to each sample. Tissues were homogenized using Precellys 24 Touch. Cycle parameters: 2 cycles: 30 seconds homogenization at 4500 rpm, 10 seconds rest. Homogenate was transferred to a microcentrifuge tube and centrifuged at 18000xrcf for 20 min at 4°C. Then, collect supernatant and transfer pellet to Precellys Lysing Kit tube. Add 84uL of 8:1:1 Acetonitrile/Methanol/Acetone to pellet and add the rest of the pre-extraction internal standards: 5µl of 1mg/ml Caffeine 13C6, 5µl of 1mg/ml D-Glucose 13C6, 5µl of 1mg/ml Oleic Acid 13C5, 1µl of 5mg/mL Isoleucine 13C6. Final pre-extraction internal standards concentrations are 50μg/mL. Homogenization cycles were repeating using Precellys 24 Touch. Centrifuge as before and add second supernatant to first round of collected supernatant. Centrifuge at 1800xrcf for 20 min once more to remove any remaining tissue debris. Collect supernatant and dry supernatant in Speedvac. Two extraction blanks were prepared in the same manner as the biological samples. Dried samples were reconstituted immediately in 0.1% formic acid in 44.75µL of HPLC-MS grade water. Post-extraction internal standards were added: 25 µl of 5mg/ml Phenylalanine 13C6, 2.5 µl of .5mg/ml Uracil 13C 15N2, 1.25 µl of 1mg/ml Arginine 13C6, 1.25 µl of 1mg/ml Serine 13C3 to each sample.

Sampleprep ID:

SP002888

Sampleprep Summary:

Retinas remained on dry ice to prevent metabolite degradation while the metabolite extraction was conducted. Tissues were transferred to 0.5mL Soft Tissue Lysing Kit Precellys tubes containing beads. Then, 84 µL of chilled 1:1 MeOH/H2O were added to Precellys tube. Pre-extraction internal standards were added to the tubes: 5µl of 1mg/ml Caffeine 13C6, 5µl of 1mg/ml D-Glucose 13C6, 5µl of 1mg/ml Oleic Acid 13C5, and 1µl of 5mg/mL Isoleucine 13C6 to each sample. Tissues were homogenized using Precellys 24 Touch. Cycle parameters: 2 cycles: 30 seconds homogenization at 4500 rpm, 10 seconds rest. Homogenate was transferred to a microcentrifuge tube and centrifuged at 18000xrcf for 20 min at 4°C. Then, collect supernatant and transfer pellet to Precellys Lysing Kit tube. Add 84uL of 8:1:1 Acetonitrile/Methanol/Acetone to pellet and add the rest of the pre-extraction internal standards: 5µl of 1mg/ml Caffeine 13C6, 5µl of 1mg/ml D-Glucose 13C6, 5µl of 1mg/ml Oleic Acid 13C5, 1µl of 5mg/mL Isoleucine 13C6. Final pre-extraction internal standards concentrations are 50μg/mL. Homogenization cycles were repeating using Precellys 24 Touch. Centrifuge as before and add second supernatant to first round of collected supernatant. Centrifuge at 1800xrcf for 20 min once more to remove any remaining tissue debris. Collect supernatant and dry supernatant in Speedvac. Two extraction blanks were prepared in the same manner as the biological samples. Dried samples were reconstituted immediately in 0.1% formic acid in 44.75µL of HPLC-MS grade water. Post-extraction internal standards were added: 25 µl of 5mg/ml Phenylalanine 13C6, 2.5 µl of .5mg/ml Uracil 13C 15N2, 1.25 µl of 1mg/ml Arginine 13C6, 1.25 µl of 1mg/ml Serine 13C3 to each sample.

Combined analysis:

Analysis ID	AN004517	AN004518
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Thermo Vanquish	Thermo Vanquish
Column	Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um)	Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um)
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	Normalized Concentrations	Normalized Concentrations

Chromatography:

Chromatography ID:	CH003393
Chromatography Summary:	Mobile Phases: NEG A: 10mM Ammonium Acetate in 95% ACN w/ .1% acetic acid NEG B: 10mM Ammonium Acetate in 50% ACN w/ .1% acetic acid POS A: 10mM Ammonium Formate in 95% ACN w/ .1% formic acid POS B: 10mM Ammonium Formate in 50% ACN w/ .1% formic acid
Instrument Name:	Thermo Vanquish
Column Name:	Thermo Accucore Amide HILIC (150 x 2.1mm, 2.6um)
Column Temperature:	35 C
Flow Gradient:	PumpModule.Pump.Pump_Pressure.AcqOn 0.000 [min] Run PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 1.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 9.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 95.0 [%] PumpModule.Pump.Curve: 5 10.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 95.0 [%] PumpModule.Pump.Curve: 5 10.500 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 15.000 [min] PumpModule.Pump.Flow.Nominal: 0.500 [ml/min] PumpModule.Pump.%B.Value: 1.0 [%] PumpModule.Pump.Curve: 5 15.000 [min] Stop Run
Flow Rate:	0.5 ml/min
Solvent A:	95% acetonitrile/5% water; 10mM Ammonium Formate; 0.1% formic acid
Solvent B:	50% acetonitrile/50% water; 10mM Ammonium Formate; 0.1% formic acid
Chromatography Type:	HILIC

MS:

MS ID:	MS004264
Analysis ID:	AN004517
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The samples were run using a Q ExactiveTM mass spectrometer coupled to a heated electrospray ionization (HESI) source. The spray voltage was set to 3.50 kV, capillary temperature to 350°C, sheath gas to 55, aux gas to 14, sweep gas to 4, and S-Lens RF Level to 30.0. The mass range was set to 67 – 1000 m/z, resolution 140,000 for full scan and 35,000 for ddMS2. AGC target was set to 1e6 for full scan and 2e5 for ddMS2. The max injection time (IT) was 100 seconds for full scan mode and 50 seconds for ddMS2. The number of microscans was 2, and normalized collision energy (NCE) was set to 20, 35, and 50. Samples were run in both positive and negative ion mode separately. The parameters for negative mode were the same except the spray voltage, which was set to 2.50 kV and capillary temperature to 380°C. Metabolites were identified from their Thermo.RAW scans using Compound DiscovererTM 3.3 software. Extraction blanks were used to determine and correct for reagent effects, allow for the creation of exclusions lists, mark background components, and filters the background components from the results table in Compound DiscovererTM 3.3. Pooled QCs were used for initial compound normalization and identification. All non-identified compounds were removed.
Ion Mode:	POSITIVE

MS ID:	MS004265
Analysis ID:	AN004518
Instrument Name:	Thermo Q Exactive Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	The samples were run using a Q ExactiveTM mass spectrometer coupled to a heated electrospray ionization (HESI) source. The spray voltage was set to 3.50 kV, capillary temperature to 350°C, sheath gas to 55, aux gas to 14, sweep gas to 4, and S-Lens RF Level to 30.0. The mass range was set to 67 – 1000 m/z, resolution 140,000 for full scan and 35,000 for ddMS2. AGC target was set to 1e6 for full scan and 2e5 for ddMS2. The max injection time (IT) was 100 seconds for full scan mode and 50 seconds for ddMS2. The number of microscans was 2, and normalized collision energy (NCE) was set to 20, 35, and 50. Samples were run in both positive and negative ion mode separately. The parameters for negative mode were the same except the spray voltage, which was set to 2.50 kV and capillary temperature to 380°C. Metabolites were identified from their Thermo.RAW scans using Compound DiscovererTM 3.3 software. Extraction blanks were used to determine and correct for reagent effects, allow for the creation of exclusions lists, mark background components, and filters the background components from the results table in Compound DiscovererTM 3.3. Pooled QCs were used for initial compound normalization and identification. All non-identified compounds were removed.
Ion Mode:	NEGATIVE