Summary of Study ST003648
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 PR002258. The data can be accessed directly via it's Project DOI: 10.21228/M8RK0K 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 | ST003648 |
| Study Title | Analysis of the role of PNPLA6 in the mouse retina |
| Study Summary | We generated PNPLA6 flox/flox CreER(+) mice, knocked out PNPLA6 by treatment with tamoxifen and isolated their retinal pigment epithelium. Lipid analysis of the retinal pigment epithelial cells was subsequently performed. |
| Institute | University of Tokyo |
| Last Name | Ono |
| First Name | Takashi |
| Address | 7-3-1, Hongo, Bunkyo-ku |
| taono-tky@umin.ac.jp | |
| Phone | 0338155411 |
| Submit Date | 2024-12-30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML |
| Analysis Type Detail | API-MS |
| Release Date | 2025-01-26 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002258 |
| Project DOI: | doi: 10.21228/M8RK0K |
| Project Title: | Function of retinal pigment epithelium in the absence of PNPLA6 |
| Project Summary: | Deletion of PNPLA6 has been reported to cause retinitis pigmentosa with neurodegeneration.Since PNPLA6 is predominantly expressed in retinal pigment epithelial cells in the retina, in this study PNPLA6 was knocked down in retinal pigment epithelial cells and its lipid composition was analysed. |
| Institute: | University of Tokyo |
| Last Name: | Ono |
| First Name: | Takashi |
| Address: | 7-3-1, Hongo, Bunkyo-ku |
| Email: | taono-tky@umin.ac.jp |
| Phone: | +81-338155411 |
Subject:
| Subject ID: | SU003778 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA398286 | PN6KO-1 | KO |
| SA398287 | PN6KO-2 | KO |
| SA398288 | PN6KO-3 | KO |
| SA398289 | PN6KO-4 | KO |
| SA398290 | C-1 | Wild |
| SA398291 | C-2 | Wild |
| SA398292 | C-3 | Wild |
| SA398293 | C-4 | Wild |
| Showing results 1 to 8 of 8 |
Collection:
| Collection ID: | CO003771 |
| Collection Summary: | We established PNPLA6 flox/flox CreER(+) mice by mating and knocking out PNPLA6 by treatment with tamoxifen. PNPLA6 flox/flox CreER(-) mice were used as a control group. The eye was excised, the corneal ring was incised under a microscope, the retina was removed and the retinal pigment epithelium was isolated bluntly. The isolated retinal pigment epithelial cells were analyzed for lipids using LC-MS/MS. |
| Sample Type: | Eye tissue |
Treatment:
| Treatment ID: | TR003787 |
| Treatment Summary: | After Pnpla6fl/flCAG-CreER (+) and Pnpla6fl/flCAG-CreER (-) were euthanized by cervical dislocation, the eyes were isolated, periocular connective tissue was removed, and the optic nerve was isolated. The cornea was separated at the corneal ring using a Vannas shear (and then the iris and lens were removed. An intact RPE sheet was removed from the underlying Bruch's membrane using a microsurgical crescent knife under a dissecting microscope. |
Sample Preparation:
| Sampleprep ID: | SP003785 |
| Sampleprep Summary: | Retinal pigment epithelium was collected from the retina with microscope. After two washes with culture medium, retinal pigment epithelial cells were carefully collected in 1.5 mL centrifuge tubes and carefully resuspended using micropipette, avoiding contamination of other tissues such as retinal debris and choroid. |
Chromatography:
| Chromatography ID: | CH004554 |
| Instrument Name: | LC-30AD |
| Column Name: | SeQuant ZIC-HILIC (100 x 2.1 mm, 3.5 µm) |
| Column Temperature: | 50°C |
| Flow Gradient: | 0–3 min 0% B; 3–6 min 0–60% B; 6–17 min 60–62.2% B; 17–17.01 min 62.2–69.8% B; 17.01–20 min 69.8–100% B; 20–23 min 100% B; 23–23.10 min 100–0% B; 23.10–26 min 0% B |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 95% Acetonitrile/5% Water; 10 mM ammonium acetate |
| Solvent B: | 50% Acetonitrile/50% Water; 20 mM ammonium acetate |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN005994 |
| Analysis Type: | MS |
| Chromatography ID: | CH004554 |
| Num Factors: | 2 |
| Num Metabolites: | 9 |
| Rt Units: | Minutes |
| Units: | nmol/10^6 cells |
