Summary of Study ST000679
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 PR000480. The data can be accessed directly via it's Project DOI: 10.21228/M8102Z This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000679 |
| Study Title | Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II |
| Study Type | MS analysis |
| Study Summary | In this experiment, vector , GCKR (WT), GCKR(P446L), PPP1R3B, TM6SF2 (WT and E167K) overexpression stable HuH-7_Lok cell lines as well as Non-target, GCKR shRNA (52621), PPP1R3B shRNA (2640), TM6SF2 shRNA (382426) knockdown HuH-7_Lok cell lines are used to do the lipidomics experiments 3 X 100 mm dishes of cells were seeded (1x106 cells/dish) for each cell line and incubated at 37? C for 24 hours, then replaced medium with delipidated serum DMEM medium. After 24 hours, treated with BSA-OA (200?M) for another 24 hours before the collection of cells Add 4mL/dish 50 mM ammonium acetate wash cells and then quench cells by adding liquid nitrogen covering all the surface of dish. Store the cell samples in -80?C freezer. |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@med.umich.edu | |
| Phone | (734) 232-8175 |
| Submit Date | 2017-06-05 |
| Num Groups | 8 |
| Total Subjects | 1 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2017-12-06 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR000480 |
| Project DOI: | doi: 10.21228/M8102Z |
| Project Title: | Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) |
| Project Type: | MS analysis |
| Project Summary: | In this study, we determine the genetic mechanism of action by which variants near PNPLA3 and PPP1R3B exert their effects on promoting NAFLD |
| Institute: | University of Michigan |
| Department: | Internal Medicine |
| Laboratory: | Speliotes Lab |
| Last Name: | Speliotes |
| First Name: | Elizabeth |
| Address: | Ann Arbor, MI |
| Email: | espeliot@umich.edu |
| Phone: | 734-647-2964 |
Subject:
| Subject ID: | SU000702 |
| Subject Type: | Human |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Human |
Factors:
Subject type: Human; Subject species: Homo sapiens (Factor headings shown in green)
| mb_sample_id | local_sample_id | Construct |
|---|---|---|
| SA038962 | S00026062 | GCKR_52621 |
| SA038963 | S00026061 | GCKR_52621 |
| SA038964 | S00026063 | GCKR_52621 |
| SA038965 | S00026066 | NT-25-9-16 |
| SA038966 | S00026065 | NT-25-9-16 |
| SA038967 | S00026064 | NT-25-9-16 |
| SA038974 | S00026070 | PNPLA3_50053 |
| SA038975 | S00026071 | PNPLA3_50053 |
| SA038976 | S00026072 | PNPLA3_50053 |
| SA038968 | S00026059 | PNPLA3(I148M) |
| SA038969 | S00026058 | PNPLA3(I148M) |
| SA038970 | S00026060 | PNPLA3(I148M) |
| SA038971 | S00026055 | PNPLA3(WT) |
| SA038972 | S00026056 | PNPLA3(WT) |
| SA038973 | S00026057 | PNPLA3(WT) |
| SA038977 | S00026069 | PPP1R3B_2640-25-9-16 |
| SA038978 | S00026067 | PPP1R3B_2640-25-9-16 |
| SA038979 | S00026068 | PPP1R3B_2640-25-9-16 |
| SA038980 | S00026074 | TM6SF2_382426 |
| SA038981 | S00026075 | TM6SF2_382426 |
| SA038982 | S00026073 | TM6SF2_382426 |
| SA038983 | S00026053 | Vector-25-9-16 |
| SA038984 | S00026054 | Vector-25-9-16 |
| SA038985 | S00026052 | Vector-25-9-16 |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO000696 |
| Collection Summary: | - |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR000716 |
| Treatment Summary: | - |
Sample Preparation:
| Sampleprep ID: | SP000709 |
| Sampleprep Summary: | - |
| Sampleprep Protocol Filename: | A004_-_Shotgun_Lipidomics.pdf |
Combined analysis:
| Analysis ID | AN001044 | AN001045 |
|---|---|---|
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | Reversed phase |
| Chromatography system | Shimadzu CTO-20A Nexera X2 | Shimadzu CTO-20A Nexera X2 |
| Column | Waters Acquity HSS T3 (50 x 2.1mm,1.8um) | Waters Acquity HSS T3 (50 x 2.1mm,1.8um) |
| MS Type | ESI | ESI |
| MS instrument type | Triple TOF | Triple TOF |
| MS instrument name | ABI Sciex 5600+ TripleTOF | ABI Sciex 5600+ TripleTOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | peak area normalized | peak area normalized |
Chromatography:
| Chromatography ID: | CH000742 |
| Instrument Name: | Shimadzu CTO-20A Nexera X2 |
| Column Name: | Waters Acquity HSS T3 (50 x 2.1mm,1.8um) |
| Column Temperature: | 55 |
| Flow Rate: | 0.400uL/min |
| Solvent A: | 40% acetonitrile/60% water; 10 mM ammonium acetate |
| Solvent B: | 10% acetonitrile/5% water/85% isopropanol; 10 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS000939 |
| Analysis ID: | AN001044 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| Analysis Protocol File: | A004_-_Shotgun_Lipidomics.pdf |
| MS ID: | MS000940 |
| Analysis ID: | AN001045 |
| Instrument Name: | ABI Sciex 5600+ TripleTOF |
| Instrument Type: | Triple TOF |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Analysis Protocol File: | A004_-_Shotgun_Lipidomics.pdf |
