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.
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 | ST001150 |
| Study Title | Metabolomics of a Mouse Model for Retinitis Pigmentosa |
| Study 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 at Chapel Hill |
| Department | Department of Cell Biology & Physiology |
| Last Name | Weiss |
| First Name | Ellen |
| Address | CB# 7545, 5340B MBRB, 111 Mason Farm Rd. Chapel Hill, NC 27599-7090 |
| erweiss@med.unc.edu | |
| Phone | 919-966-7683 |
| Submit Date | 2019-03-18 |
| Analysis Type Detail | LC-MS |
| Release Date | 2019-07-17 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
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 |
|---|---|---|
| SA079835 | All_pool_QC3 | QC Pool |
| SA079836 | All_pool_QC1 | QC Pool |
| SA079837 | All_pool_QC2 | QC Pool |
| SA079838 | RD10-RCL-D-110113-RT-3 | RD10-RCL-D |
| SA079839 | RD10-RCL-D-110913-RT-3 | RD10-RCL-D |
| SA079840 | RD10-RCL-D-111013-RT-3 | RD10-RCL-D |
| SA079841 | RD10-RCL-D-100913-RT-2 | RD10-RCL-D |
| SA079842 | RD10-RCL-D-111013-RT-2 | RD10-RCL-D |
| SA079843 | RD10-RCL-L-110113-RT-2 | RD10-RCL-L |
| SA079844 | RD10-RCL-L-110113-RT-1 | RD10-RCL-L |
| SA079845 | RD10-RCL-L-111013-RT-1 | RD10-RCL-L |
| SA079846 | RD10-RCL-L-110913-RT-1 | RD10-RCL-L |
| SA079847 | RD10-RCL-L-110913-RT-2 | RD10-RCL-L |
| SA079848 | RD10-RCL-L-100913-RT-1 | RD10-RCL-L |
| SA079849 | RD10-RD-D-120513-RT-1 | RD10-RD-D |
| SA079850 | RD10-RD-D-120813-RT-1 | RD10-RD-D |
| SA079851 | RD10-RD-D-120813-RT-2 | RD10-RD-D |
| SA079852 | RD10-RD-D-120813-RT-3 | RD10-RD-D |
| SA079853 | RD10-RD-D-120513-RT-2 | RD10-RD-D |
| SA079854 | RD10-RD-D-120813-RT-4 | RD10-RD-D |
| SA079855 | WT-RCL-D-111713-RT-2 | WT-RCL-D |
| SA079856 | WT-RCL-D-111113-RT-3 | WT-RCL-D |
| SA079857 | WT-RCL-D-111013-RT-3 | WT-RCL-D |
| SA079858 | WT-RCL-D-101513-RT-3 | WT-RCL-D |
| SA079859 | WT-RCL-D-111113-RT-2 | WT-RCL-D |
| SA079860 | WT-RCL-L-111113-RT-1 | WT-RCL-L |
| SA079861 | WT-RCL-L-111713-RT-1 | WT-RCL-L |
| SA079862 | WT-RCL-L-101513-RT-1 | WT-RCL-L |
| SA079863 | WT-RCL-L-101513-RT-2 | WT-RCL-L |
| SA079864 | WT-RCL-L-111013-RT-2 | WT-RCL-L |
| SA079865 | WT-RCL-L-111013-RT-1 | WT-RCL-L |
| SA079866 | WT-RD-D-121213-RT-2 | WT-RD-D |
| SA079867 | WT-RD-D-121213-RT-1 | WT-RD-D |
| SA079868 | WT-RD-D-011614-RT-2 | WT-RD-D |
| SA079869 | WT-RD-D-011614-RT-1 | WT-RD-D |
| SA079870 | WT-RD-D-120513-RT-1 | WT-RD-D |
| SA079871 | WT-RD-D-120513-RT-2 | WT-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 |
