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

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Study IDST000679
Study TitleFunctional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II
Study TypeMS analysis
Study SummaryIn 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
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Emailmkachman@med.umich.edu
Phone(734) 232-8175
Submit Date2017-06-05
Num Groups8
Total Subjects1
Raw Data AvailableYes
Raw Data File Type(s).wiff
Analysis Type DetailLC-MS
Release Date2017-12-06
Release Version1
Maureen Kachman Maureen Kachman
https://dx.doi.org/10.21228/M8102Z
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA038962S00026062GCKR_52621
SA038963S00026061GCKR_52621
SA038964S00026063GCKR_52621
SA038965S00026066NT-25-9-16
SA038966S00026065NT-25-9-16
SA038967S00026064NT-25-9-16
SA038974S00026070PNPLA3_50053
SA038975S00026071PNPLA3_50053
SA038976S00026072PNPLA3_50053
SA038968S00026059PNPLA3(I148M)
SA038969S00026058PNPLA3(I148M)
SA038970S00026060PNPLA3(I148M)
SA038971S00026055PNPLA3(WT)
SA038972S00026056PNPLA3(WT)
SA038973S00026057PNPLA3(WT)
SA038977S00026069PPP1R3B_2640-25-9-16
SA038978S00026067PPP1R3B_2640-25-9-16
SA038979S00026068PPP1R3B_2640-25-9-16
SA038980S00026074TM6SF2_382426
SA038981S00026075TM6SF2_382426
SA038982S00026073TM6SF2_382426
SA038983S00026053Vector-25-9-16
SA038984S00026054Vector-25-9-16
SA038985S00026052Vector-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)
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
  
MS ID:MS000940
Analysis ID:AN001045
Instrument Name:ABI Sciex 5600+ TripleTOF
Instrument Type:Triple TOF
MS Type:ESI
Ion Mode:POSITIVE
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