Summary of Study ST001150

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 PR000769. The data can be accessed directly via it's Project DOI: 10.21228/M88T11 This work is supported by NIH grant, U2C- DK119886.

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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 IDST001150
Study TitleMetabolomics of a Mouse Model for Retinitis Pigmentosa
Study SummaryRetinitis pigmentosa (RP) is a degenerative disease of the retina that affects approximately 1 million people worldwide. There are multiple genetic causes of this disease, for which, at present, there are no effective therapeutic strategies. We utilized broad spectrum metabolomics to identify perturbations in the metabolism of the rd10 mouse, a genetic model for RP. C57BL/6J and rd10 mice were raised in cyclic light followed by either light or dark adaptation at postnatal day (P) 18, an early stage in the degeneration process. Mice raised entirely in the dark until P18 were also evaluated. After euthanasia, retinas were removed and extracted for analysis by ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-QTOF-MS).
Institute
University of North Carolina at Chapel Hill
DepartmentDepartment of Cell Biology & Physiology
Last NameWeiss
First NameEllen
AddressCB# 7545, 5340B MBRB, 111 Mason Farm Rd. Chapel Hill, NC 27599-7090
Emailerweiss@med.unc.edu
Phone919-966-7683
Submit Date2019-03-18
Analysis Type DetailLC-MS
Release Date2019-07-17
Release Version1
Ellen Weiss Ellen Weiss
https://dx.doi.org/10.21228/M88T11
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR000769
Project DOI:doi: 10.21228/M88T11
Project Title:Metabolomics of a Mouse Model for Retinitis Pigmentosa
Project Summary:Retinitis pigmentosa (RP) is a degenerative disease of the retina that affects approximately 1 million people worldwide. There are multiple genetic causes of this disease, for which, at present, there are no effective therapeutic strategies. We utilized broad spectrum metabolomics to identify perturbations in the metabolism of the rd10 mouse, a genetic model for RP. C57BL/6J and rd10 mice were raised in cyclic light followed by either light or dark adaptation at postnatal day (P) 18, an early stage in the degeneration process. Mice raised entirely in the dark until P18 were also evaluated. After euthanasia, retinas were removed and extracted for analysis by ultra-performance liquid chromatography-time of flight-mass spectrometry (UPLC-QTOF-MS).
Institute:University of North Carolina
Laboratory:ERCMRC
Last Name:Sumner
First Name:Susan
Address:NRI, 500 Laureate Way, Kannapolis, NC, 28081, USA
Email:susan_sumner@unc.edu
Phone:704-250-5066
Funding Source:NIDDK U24DK097193 (Sumner, PI); Supplement to NEI R01EY12224 (Weiss, PI)

Subject:

Subject ID:SU001215
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:rd10 and C57BL/6J
Age Or Age Range:P18
Animal Animal Supplier:Jackson Laboratory

Factors:

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

mb_sample_id local_sample_id Condition
SA079835All_pool_QC3QC Pool
SA079836All_pool_QC1QC Pool
SA079837All_pool_QC2QC Pool
SA079838RD10-RCL-D-110113-RT-3RD10-RCL-D
SA079839RD10-RCL-D-110913-RT-3RD10-RCL-D
SA079840RD10-RCL-D-111013-RT-3RD10-RCL-D
SA079841RD10-RCL-D-100913-RT-2RD10-RCL-D
SA079842RD10-RCL-D-111013-RT-2RD10-RCL-D
SA079843RD10-RCL-L-110113-RT-2RD10-RCL-L
SA079844RD10-RCL-L-110113-RT-1RD10-RCL-L
SA079845RD10-RCL-L-111013-RT-1RD10-RCL-L
SA079846RD10-RCL-L-110913-RT-1RD10-RCL-L
SA079847RD10-RCL-L-110913-RT-2RD10-RCL-L
SA079848RD10-RCL-L-100913-RT-1RD10-RCL-L
SA079849RD10-RD-D-120513-RT-1RD10-RD-D
SA079850RD10-RD-D-120813-RT-1RD10-RD-D
SA079851RD10-RD-D-120813-RT-2RD10-RD-D
SA079852RD10-RD-D-120813-RT-3RD10-RD-D
SA079853RD10-RD-D-120513-RT-2RD10-RD-D
SA079854RD10-RD-D-120813-RT-4RD10-RD-D
SA079855WT-RCL-D-111713-RT-2WT-RCL-D
SA079856WT-RCL-D-111113-RT-3WT-RCL-D
SA079857WT-RCL-D-111013-RT-3WT-RCL-D
SA079858WT-RCL-D-101513-RT-3WT-RCL-D
SA079859WT-RCL-D-111113-RT-2WT-RCL-D
SA079860WT-RCL-L-111113-RT-1WT-RCL-L
SA079861WT-RCL-L-111713-RT-1WT-RCL-L
SA079862WT-RCL-L-101513-RT-1WT-RCL-L
SA079863WT-RCL-L-101513-RT-2WT-RCL-L
SA079864WT-RCL-L-111013-RT-2WT-RCL-L
SA079865WT-RCL-L-111013-RT-1WT-RCL-L
SA079866WT-RD-D-121213-RT-2WT-RD-D
SA079867WT-RD-D-121213-RT-1WT-RD-D
SA079868WT-RD-D-011614-RT-2WT-RD-D
SA079869WT-RD-D-011614-RT-1WT-RD-D
SA079870WT-RD-D-120513-RT-1WT-RD-D
SA079871WT-RD-D-120513-RT-2WT-RD-D
Showing results 1 to 37 of 37

Collection:

Collection ID:CO001209
Collection Summary:C57BL/6J and rd10 mice were raised under varying light conditions in standard housing, temperature and access to food and water. Some mice were raised under normal light/dark cycle at ambient light levels of approximately 80 lux. At 18 days after birth, mice were exposed to 250 lux for 3 h (light-adapted) followed by euthanasia using cervical dislocation. The eyes were enucleated and the retinas dissected in PBS in the light under a microscope, followed by rapid freezing by dropping them individually into a container filled with liquid nitrogen. Each set of samples were pooled in liquid nitrogen. Other mice raised in cyclic light were adapted overnight at P17 in complete darkness (dark-adapted) before euthanasia at P18. Using infrared goggles and an infrared microscope, these retinas were processed similarly as light-adapted samples except that all procedures were performed in the dark. Mice raised in total darkness were euthanized at P18 and dissected in the dark using infrared goggles and an infrared microscope.
Sample Type:Retina

Treatment:

Treatment ID:TR001230
Treatment Summary:C57BL/6J and rd10 mice were raised under varying light conditions in standard housing, temperature and access to food and water. Some mice were raised under normal light/dark cycle at ambient light levels of approximately 80 lux. At 18 days after birth, mice were exposed to 250 lux for 3 h (light-adapted) followed by euthanasia. Other mice raised in cyclic light were adapted overnight at P17 in complete darkness (dark-adapted) before euthanasia at P18. Mice raised in total darkness were euthanized at P18.

Sample Preparation:

Sampleprep ID:SP001223
Sampleprep Summary:Each sample was homogenized in buffer containing 50:50 acetonitrile:water at a ratio of 1mg:25 µl tissue:buffer. A 320 µl aliquot of homogenate (12.8 mg tissue equivalent) was transferred to a tube and centrifuged. The supernatant was dried and re-suspended in 100 µl 95:5 H2O:methanol for UPLC-TOF-MS analysis.

Combined analysis:

Analysis ID AN001897 AN001898
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um) Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
MS Type ESI ESI
MS instrument type QTOF QTOF
MS instrument name Waters Synapt-G2-Si Waters Synapt-G2-Si
Ion Mode NEGATIVE POSITIVE
Units m/z_retention time m/z_retention time

Chromatography:

Chromatography ID:CH001374
Chromatography Summary:Reversed-Phase Gradient Seperation
Instrument Name:Waters Acquity
Column Name:Waters Acquity BEH HSS T3 (100 x 2.1mm,1.8um)
Column Pressure:6,000-10,000 psi
Column Temperature:50 °C
Flow Gradient:Time(min) Flow Rate(mL/min) %A %B Curve 1. Initial 0.400 99.0 1.0 6 2. 1.00 0.400 99.0 1.0 6 3. 16.00 0.400 1.0 99.0 6 4. 20.00 0.400 1.0 99.0 6 5. 20.50 0.400 99.0 1.0 6 6. 22.00 0.400 99.0 1.0 6
Flow Rate:0.4 mL/min
Injection Temperature:8 °C
Internal Standard:L-Tryptophan-d5
Chromatography Type:Reversed phase

MS:

MS ID:MS001753
Analysis ID:AN001897
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
MS Comments:MassLynx 4.1
Ion Mode:NEGATIVE
Capillary Temperature:110 °C
Capillary Voltage:1.0 kV
Collision Energy:4
Fragmentation Method:CID
Helium Flow:180
Ionization:ES-
Mass Accuracy:5 ppm
Source Temperature:110 °C
Dataformat:Continuum
Desolvation Gas Flow:800 L/Hr
Desolvation Temperature:400 °C
Resolution Setting:20000
Scan Range Moverz:50-1000 m/z
Scanning Cycle:1.0 s
Tube Lens Voltage:75
  
MS ID:MS001754
Analysis ID:AN001898
Instrument Name:Waters Synapt-G2-Si
Instrument Type:QTOF
MS Type:ESI
MS Comments:MassLynx 4.1
Ion Mode:POSITIVE
Capillary Temperature:110 °C
Capillary Voltage:1.0 kV
Collision Energy:4
Fragmentation Method:CID
Helium Flow:180
Ionization:ES+
Mass Accuracy:5 ppm
Source Temperature:110 °C
Dataformat:Continuum
Desolvation Gas Flow:1000 L/Hr
Desolvation Temperature:400 °C
Resolution Setting:20000
Scan Range Moverz:50-1000 m/z
Scanning Cycle:1.0 s
Tube Lens Voltage:75
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