Browse
Submit Data
Databases
API
Help

Dataset Information

58 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

E-GEOD-51704

ABSTRACT: Gene expression profiling of KLF5, GATA4 and GATA6 knock down in YCC3/AGS/KATOIII cell lines

OTHER RELATED OMICS DATASETS IN: PRJNA224584PRJNA150983PRJNA224585PRJNA122965PRJNA144797PRJNA152559PRJNA224586

PROVIDER: E-GEOD-51704 | ExpressionAtlas | 2015-07-27

REPOSITORIES: ExpressionAtlas

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	E-GEOD-51704-analysis-methods.tsv	Tabular
	E-GEOD-51704-atlasExperimentSummary.Rdata	Rdata
	E-GEOD-51704-configuration.xml	Xml
	E-GEOD-51704-percentile-ranks.tsv	Tabular
	E-GEOD-51704.condensed-sdrf.tsv	Tabular

Items per page:

1 - 5 of 194

Similar Datasets

Expression profiling of isogenic A549 cell lines with and without ELF3 knock-down

Project description:Expression profiling of isogenic A549 cell lines with and without ELF3 knock-down

| PRJNA565714 | ENA

Expression data of knock down LOC441461 in MKN74 cell lines

Project description:Expression data of knock down LOC441461 in MKN74 cell lines

| PRJNA797275 | ENA

Homo sapiens

Project description:Gene expression profiling of KLF5, GATA4 and GATA6 knock down in YCC3/AGS/KATOIII cell lines

| PRJNA224586 | ENA

KDM7 is a dual demethylase for histone H3 lysines 9 and 27 and functions in brain development

Project description:The roles of histone demethylase KDM7 in gene expression were analyzed by gene expression profiling experiments with mouse neuroblastoma cell line Neuro2A. Keywords: mouse neuroblastoma, Neuro2A, gene expression profiling, microarray, Affimetrix M430 2.0 chip In order to examine the effect of KDM7 in gene expression, we generated stable KDM7 knockdown cell lines in mouse neuroblastoma cell line Neuro2A. Total RNAs were extracted from 5 cell lines (parental cells: Neuro2A, empty vector: Neuro2A transfected with empty vector, EGFP KD: Neuro2A transfected with vector for EGFP knock down, KDM7 KD1: Neuro2A transfected with vector 1 for KDM7 knock down, and KDM7 KD2: Neuro2A transfected with vector 2 for KDM7 knock down) and analyzed for gene expression profiles using Affymetrix platform.

2010-03-06 | E-GEOD-17494 | biostudies-arrayexpress

Enhanced snoMEN vectors facilitate establishment of GFP–HIF-1? protein replacement human cell lines

Project description:The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1? replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy.

2017-03-31 | MSV000080828 | MassIVE

Gene expression profiling of Cav1 knock down in murine hepatic stellate cell

Project description:Gene expression profiling of Cav1 knock down in murine hepatic stellate cell

| PRJNA953968 | ENA

Homo sapiens

Project description:Knock-down of BCL6 expression in human Diffuse Large B-Cell Lymphoma cell lines

| PRJNA196519 | ENA

Consequence of knock down of CBX7 in multiple cell lines

Project description:Consequence of knock down of CBX7 in multiple cell lines

| PRJNA1068482 | ENA

ena-DATASET-DKFZ-IBIOS-16-07-2015-15:45:02:488-51 - samples

Project description:Despite the established role of the transcription factor MYC in cancer, little is known about the impact of a new class of transcriptional regulators, the long non-coding RNAs (lncRNAs), on the way MYC is able to influence cellular transcriptome. To this aim we have intersected RNA-sequencing data from two MYC-inducible cell lines and from a cohort of 91 mature B-cell lymphomas carrying, or not carrying, genetic variants resulting in MYC over-expression. By this approach, we identified 13 lncRNAs differentially expressed in IG-MYC-positive Burkitt lymphoma and regulated in the same direction by MYC in the model cell lines. Among them we focused on a lncRNA that we named MINCR, for MYC-Induced long Non-Coding RNA, showing a strong correlation with MYC expression in MYC-positive lymphomas and also in pancreatic ductal adenocarcinomas. To understand its cellular role we performed RNA interference (RNAi) experiments and found that MINCR knock-down is associated with a reduction in cellular viability, due to an impairment in cell cycle progression. Differential gene expression analysis following RNAi showed a strongly significant enrichment of cell cycle genes among the genes down-regulate following MINCR knock-down. Interestingly these genes are enriched in MYC binding sites in their promoters, suggesting that MINCR acts as a modulator of MYC transcriptional program. Accordingly, following MINCR knock-down, we observed a reduction in the binding of MYC to the promoters of selected cell cycle genes. Finally we provide evidences that down-regulation of AURKA, AURKB and CTD1 may explain the reduction in cellular proliferation observed upon MINCR knock-down. We therefore suggest that MINCR is a newly identified player in the MYC transcriptional network able to control the expression of cell cycle genes.

| EGAD00001001441 | EGA

Enhanced snoMEN vectors facilitate establishment of GFP–HIF-1α protein replacement human cell lines

Project description:The snoMEN (snoRNA Modulator of gene ExpressioN) vector technology was developed from a human box C/D snoRNA, HBII-180C, which contains an internal sequence that can be manipulated to make it complementary to RNA targets, allowing knock-down of targeted genes. Here we have screened additional human nucleolar snoRNAs and assessed their application for gene specific knock-downs to improve the efficiency of snoMEN vectors. We identify and characterise a new snoMEN vector, termed 47snoMEN, that is derived from box C/D snoRNA U47, demonstrating its use for knock-down of both endogenous cellular proteins and G/YFP-fusion proteins. Using multiplex 47snoMEM vectors that co-express multiple 47snoMEN in a single transcript, each of which can target different sites in the same mRNA, we document >3-fold increase in knock-down efficiency when compared with the original HBII-180C based snoMEN. The multiplex 47snoMEM vector allowed the construction of human protein replacement cell lines with improved efficiency, including the establishment of novel GFP–HIF-1α replacement cells. Quantitative mass spectrometry analysis confirmed the enhanced efficiency and specificity of protein replacement using the 47snoMEN-PR vectors. The 47snoMEN vectors expand the potential applications for snoMEN technology in gene expression studies, target validation and gene therapy.

2016-05-06 | PXD003622 | 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