Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II

ABSTRACT: 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.

ORGANISM(S): Human Homo Sapiens

TISSUE(S): Cultured Cells

DISEASE(S): Fatty Liver Disease

SUBMITTER: Maureen Kachman

PROVIDER: ST000679 | MetabolomicsWorkbench | Mon Jun 05 00:00:00 BST 2017

REPOSITORIES: MetabolomicsWorkbench

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	mwtab	Other

Items per page:

1 - 1 of 1

Similar Datasets

Functional genomics study on Non Alcoholic fatty liver disease (NAFLD)

Project description: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.

2017-06-05 | ST000678 | MetabolomicsWorkbench

Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part III

2017-06-05 | ST000680 | MetabolomicsWorkbench

Metabolomics Workbench ST000678 - GNPS - Functional genomics study on Non Alcoholic fatty liver disease (NAFLD)

2018-08-02 | MSV000082708 | GNPS

Metabolomics Workbench ST000680 - GNPS - Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part III

2018-08-02 | MSV000082706 | GNPS

Metabolomics Workbench ST000679 - GNPS - Functional genomics study on Non Alcoholic fatty liver disease (NAFLD) - part II

2018-08-02 | MSV000082695 | GNPS

Lipidomics analysis for human liver cell lines

Project description:On day 1, seed 1 million cells/dish Huh7_Lok cells (vector, GCKR(WT), GCKR(P446L), Non-Target, GCKR KD and PPP1R3B/OE) in 100 mm dishes with DMEM complete medium and incubate at 37C for 24 h. On day 2, replace DMEM medium with delipidated serum medium for these cells and incubate for another 24 h. On day 3, add heated Oleic Acid-Albumin into each dish at final concentration of 200?M for 24h. On day 4, collect cells with Trypsin/EDTA lysis and count cells with automated cell counter and calculate total cell numbers in each sample, then centrifuge cells down and take out the supernatant and keep cells in -80 C freezer.

2017-06-05 | ST000685 | MetabolomicsWorkbench

Metabolomics Workbench ST000685 - GNPS - Lipidomics analysis for human liver cell lines

2018-08-02 | MSV000082719 | GNPS

Development of gene expression signatures of CTCF-expressing vs CTCF-depleted hepatocellular carcinoma cells

Project description:To understand the functional role of CTCF in the oncogenesis of HCC, we constructed lentiviruses expressing control shRNA (shCont) or shRNA agains CTCF (shCTCF) and transduced them into PLC5 cells respectively. After 24 hours, cells were cultered in puromycin containing medium (5 ug) for another 24 hours. Cells were returned to normal medium for another 48 hours before total mRNAs were corrected for whole genome gene expression array analysis. Expression of FoxM1 gene from this signature was quantified in an independent set of RNA samples by real-time PCR, confirming differntial expression of this gene in shCTCF expressing cells.

2017-09-30 | GSE100533 | GEO

mRNA-sequencing for MM.1S cells that were treated with pomalidomide or were expressing shRNA against ARID2 or Aiolos.

Project description:To dissect the roles of ARID2 and Aiolos in pomalidomide-induced transcriptional changes, we performed mRNA-sequencing of MM.1S cells expressing shRNA against ARID2 or Aiolos and compared them with MM.1S cells that were treated with pomalidomide for 24, 48, or 72 hours.

2020-07-22 | GSE126463 | GEO

Impact of STAU1 depletion on the protein expression profile of rhabdomyosarcoma cell lines

Project description:Two human rhabdomyosarcoma cell lines (RD, RH36, RH30, and RH18) and one none-transformed skeletal muscle cell line (HSMM-C3) cell line were studied for the impact of Staufen1 depletion on their protein expression profile. Proteomics was performed for control and Staufen1 knockdown cells (n=3). For this, we generated STAU1 knockdown cell lines using a mixture of three independent STAU1-targeting lentiviral-shRNA constructs. cells were cultured for 72 hours and then protein extraction was performed as follow: Cells were lysed in 1X RIPA buffer (20 mM Tris-HCl (pH 7.5), 150mM NaCl, 1mM Na2- EDTA, 1mM EGTA, 1% NP-40, 1% sodium deoxycholate, 2.5 mM sodium pyrophosphate, 1mM β-glycerophosphate, 1mM Na3 VO4, 1µg/ml leupeptin). Protein concentration was tested according to the BCA assay protocol (Thermofisher Scientific) and samples were used in proteomics experiment.

2023-10-22 | PXD042156 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data