Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

89 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression analysis of TRIM5 KD in the THP1 cell line

ABSTRACT: We had evidence that TRIM5 regulates signal transduction, specifically NFkB and MAPK pathways. To test the role of endogenous TRIM5 we used the myelomonocytic leukemia cell line THP1. These cells were transduced with a lentiviral vector that delivers a miRNA engineered to knockdown TRIM5. The vector also encoded a puromycin-resistance cassette and transduced cells were selected in poold with puromycin. As a control, cells were transduced with a vector targeting luciferase instead of TRIM5. After selection in puromycin, the TRIM5 KD and Luciferase KD cells were differentiated into macrophages by treatment with PMA. 3 days later, RNA was harvested for analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Jeremy Luban

PROVIDER: E-GEOD-25041 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Gene expression analysis of TRIM5 KD in the THP1 cell line

Project description:We had evidence that TRIM5 regulates signal transduction, specifically NFkB and MAPK pathways. To test the role of endogenous TRIM5 we used the myelomonocytic leukemia cell line THP1. These cells were transduced with a lentiviral vector that delivers a miRNA engineered to knockdown TRIM5. The vector also encoded a puromycin-resistance cassette and transduced cells were selected in poold with puromycin. As a control, cells were transduced with a vector targeting luciferase instead of TRIM5.

2010-11-02 | GSE25041 | GEO

Linezolid Exerts Greater Bacterial Clearance but No Modification of Host Lung Gene Expression Profiling: a Mouse MRSA Pneumonia Model

Project description:Using the stringent criteria (fold change ≥ 1.5 up or down, P < 0.01, FDR < 0.05) to filter significantly differentially expressed genes, we did not identify any genes whose expression levels were significantly different between the PBS and PBS+LZD groups or between the LAC and LAC+LZD at Day 1 or Day 3 post MRSA infection. However, a remarkable difference was demonstrated (Figure 5A) between PBS and LAC groups at either Day 1 or Day 3 post MRSA infection. Four independent mouse lung tissue samples at Day 1 and Day 3 post MRSA infection with and without Linezolid therapy were randomly selected from each group for microarray analysis.

2014-04-10 | E-GEOD-46071 | biostudies-arrayexpress

Gene Expression in Mutant P0 Cre Dicer Mouse Sciatic Nerves

Project description:The hypothesis is that genes involved in the immature schwann cell and promyelinating state will be upregulated and genes that are involved in the myelnating state will be down regulated. Bioconductor limma package [1,2,3,4] was used to preprocess 6 samples from mouse tissue-cultured cells, which are hybridized to Mouse WG-6 version 2 Illumina Array. To remove batch effects, the complete dataset were normalized by RMA. Before doing statistical analysis, we filter the probe-sets by present/absent calls using the Wilcoxon signed rank-based algorithm. 18,420 genes out of 45,281 genes were kept and the remaining ones were removed as âAbsentâ to reduce false positive rate. We identified differentially expressed gene list by fitting linear models to the normalized expression values. The empirical Bayes shrinkage was applied to t-statistics using the limma package in Bioconductor. In general, selected genes have greater than 2.0 fold-change and less than 0.05 fdr adjusted p-value.

2010-06-16 | E-GEOD-16741 | biostudies-arrayexpress

The effects of knockdown of PML by different individual siRNAs in HUVEC cells

Project description:To study the potential target genes regulated by PML in endothelial cells, we carried out siRNA-mediated knockdown of PML in HUVEC cells. To eliminate the off-target effects of siRNAs, we utilized two different siRNAs. Only the genes changed in the same pattern following both siRNAs transfection are considered as potential PML-knockdown responsive genes. The experiment is one-factor (siRNA) with three ranks (siCtrl, siPML-1, siPML-2). We included technical duplicates for each sample. To minimize systemic errors assoicated with technique, we distributed the duplicates on two different microarray chips.

2012-05-30 | E-GEOD-29238 | biostudies-arrayexpress

miR-34a targets PDGFRA in proneural malignant glioma

Project description:To identify potential targets of miR-34a, we performed transcriptional profiling on proneural TS543 GBM cells, focusing on mRNAs whose levels decreased in response to miR-34a transfection as compared to control oligonucleotide. Proneural TS543 GBM cells were transfected with 100 nM hsa-miR-34a or control oligonucleotide using Hiperfect transfection reagent (Qiagen). After 3 days, RNA was isolated and expression analyses were performed using Illumina HT-12 bead array. The microarray dataset was normalized using a variance stable normalization (VSN) procedure in the ‘lumi’ package from the Bioconductor framework.

2012-03-26 | E-GEOD-34242 | biostudies-arrayexpress

Analysis of miR-203 regulated genes during IFNalpha treatment

Project description:The goal of this experiment was to determine gene expression changes during IFNα treatment as the result of expression or inhibition of miR-203 in A549 cells. The gene expression profiling experiment was performed with 4 groups (mock infected, IFNα treated, IFNα treated in the presence of exogenous miR-203, and IFNα treated in the presence of miR-203 inhibitor) with 3 biological replicates for each group. Total RNA was purified from A549 cells that were untreated of treated with IFNα (1000 units/mL) alone or in the presence of miR-203 mimic or inhibitor for 10 hours.

2013-06-20 | E-GEOD-47866 | biostudies-arrayexpress

Identification of miR-203 Regulated Genes During Sendai Virus Infection

Project description:The goal of this experiment was to determine gene expression changes during Sendai virus infection as the result of expression or inhibition of miR-203 in A549 cells. The gene expression profiling experiment was performed with 4 groups (mock infected, Sendai virus infected, Sendai virus infeceted in the presence of exogenous miR-203, and Sendai virus infected in the presence of miR-203 inhibitor) with 3 biological replicates for each group. Total RNA was purified from A549 cells that were mock infected or infected with Sendai virus (Cantell strain, 5pfu/cell) alone or in the presence of miR-203 mimic or inhibitor for 10 hours.

2013-06-20 | E-GEOD-47865 | biostudies-arrayexpress

Gene expression changes due to influenza virus induced miRNAs

Project description:The goal of this experiment was to determine gene expression changes during influenza A virus infection as the result of expression influenza virus inducible miRNAs in A549 cells. The gene expression profiling experiment was performed with 4 groups (mock infected, influenza A virus infected, influenza A virus infected in the presence of exogenous miR-141, miR-374b, miR-449b, miR-518b, and miR-1263, and influenza A virus infected in the presence of exogenous miR-147b, miR-190b, miR-199a, miR-512-5p, and miR-874 with 3 biological replicates for each group. Total RNA was purified from A549 cells that were mock infected or infected with influenza A virus (A/WSN/33, 5pfu/cell) alone or in the presence of miRNA mimics 10 hours after treatment.

2013-09-15 | E-GEOD-47937 | biostudies-arrayexpress

The effect of listening to music on human transcriptome

Project description:The aim of the dataset was to study the effect of music exposure on human blood transcriptome. Total RNAs from peripheral blood of samples were compared before and after listening to a 20 minutes of classical music. Samples were collected from 48 samples before and after music exposure.

2015-04-13 | E-GEOD-48624 | biostudies-arrayexpress

Notch signaling regulates neural crest differentiation from human pluripotent stem cells

Project description:The aim of the dataset was to study on genome-wide level the effect of Notch inhibition in gene expression on neural crest differentiation of human embryonic stem cells under chemically defined conditions. Total RNA from hESCs, hESC-derived neural crest, hESC-derived neural crest+DAPT, and hESC-derived neural stem cells was collected and compared at their global gene expression level. Samples from 3 biological replicates were analysed.

2014-03-03 | E-GEOD-53203 | biostudies-arrayexpress

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