Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

ABSTRACT: The microarray experiments were carried out using a long oligonucleotide DNA microarray that represent all 5363 P. falciparum genes with one oligonucleotide per 1.9kb of coding sequence on average (Hu et al. 2007). Total 247 microarray experiments were carried out including 29-drug treatment time courses with 20 compounds and corresponding untreated controls from different drug or inhibitor treatment. Data of each drug/inhibitor experiment were normalized using a linear normalization and background filtering as implemented by the NOMAD database (http://derisilab.ucsf.edu).

ORGANISM(S): Plasmodium falciparum

PROVIDER: GSE19468 | GEO | 2009/12/16

SECONDARY ACCESSION(S): PRJNA120341

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum

Project description:The microarray experiments were carried out using a long oligonucleotide DNA microarray that represent all 5363 P. falciparum genes with one oligonucleotide per 1.9kb of coding sequence on average (Hu et al. 2007). Total 247 microarray experiments were carried out including 29-drug treatment time courses with 20 compounds and corresponding untreated controls from different drug or inhibitor treatment. Data of each drug/inhibitor experiment were normalized using a linear normalization and background filtering as implemented by the NOMAD database (http://derisilab.ucsf.edu). Time-series sampling and experiments with synchronized ex vivo culturing parasites. Each experiment has treatment and controls, and starts at a specific time of post invasion. For an example of quinine treatment, the treatments start from late ring stage through trophozoite stage of the parasites. First, IC50 is determined by drug assay with synchronized parasites (5% parasiteomia and 2% RBC). Second, synchronized parasite cultures are splitted into 12 flasks (75ml culture/flask) for a 6 time-point time-series experiment. 6 flasks are treated with quinine (final concentration is IC50) and 6 flasks are negative controls. 1,2,4,6,8 and 10 hrs after the treatment, parasites in each flask were harvested for total RNA isolation and microarray hybridizaiton.

2010-05-18 | E-GEOD-19468 | biostudies-arrayexpress

Differentially Expressed Genes for Atrial Fibrillation Identified using RNA Sequencing from Paired Human Left and Right Atrial Appendages.

Project description:Next Generation RNA Sequencing was carried out on human paired left and right atrial appendages from patients with and without Atrial Fibrillation. EdgeR software was used to show a total of 247 genes were found to have significant differential expression between left and right atria.

2019-03-13 | GSE128188 | GEO

Polysome profiling RNAseq of cells transfected with an oligonucleotide targeting the ES6S region of the 40S subunit

Project description:Polysome profiling experiments were carried out to identify the mRNAs that have altered the translation efficiency (counts in polysomal fraction/counts in monosomal fractions) in the presence of an oligonucleotide targeting a specific region of the ribosomal RNA, to study the implication of this region in the translation of specific mRNAs

2019-12-10 | GSE129651 | GEO

Assessing the importance of target type for oligonucleotide microarray experiments

Project description:Assessing the importance of target type for oligonucleotide microarray experiments

| PRJNA131559 | ENA

Effect of ILB on Gene expression in SHSY5Y neuroblastoma cells

Project description:The experiments were carried out to further understand the mechanism of action of ILB, a low molecular weight dextran sulphate, in neuronal cell. The experiments were carried out with ILB concentrations that are relevant to the therapeutic concentrations of the drug. The results indicate that ILB regulates the expression of genes to enhance cell survival and differentiation is a dose dependent manner. Upstream regulator analysis indicates that the gene expression changes are due to enhanced activity of growth factors and cytokines.

2022-08-02 | GSE210027 | GEO

Effect of ILB on Gene expression in Schwann like cells

Project description:The experiments were carried out to further understand the mechanism of action of ILB, a low molecular weight dextran sulphate, in glial cell. The experiments were carried out with ILB concentrations that are relevant to the therapeutic concentrations of the drug. The results indicate that ILB regulates the expression of genes to enhance cell survival and differentiation is a dose dependent manner. Upstream regulator analysis indicates that the gene expression changes are due to enhanced activity of growth factors and cytokines.

2022-08-02 | GSE210028 | GEO

Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]

Project description:Chromatin immunoprecipitation and microarray hybridization (ChIP-chip) experiments were carried out for all 8 FFRPs in H. salinarum NRC-1.

2014-10-03 | GSE62051 | GEO

Profiling of plant miRNAs induced by drought stress in the rice plant

Project description:Expression profiles were analyzed between drought stress and normal watered control at the tillering and inflorescence stages. 1. We applied microarray analysis to detect drought-stress-regulated miRNAs from tillering to inflorescence-forming stages in rice. 2. Three time courses at the tillering stage and two time courses at the inflorescence-forming stage. Two replicates were carried out in each time course.

2011-10-25 | E-GEOD-14246 | biostudies-arrayexpress

Different gene expression between CDK5 knocking down and control colorectal cancer cell line HCT116

Project description:We sought to find out the molecular mechanism of CDK5 displayed in colorectal cancer. Microarray experiments were carried out to identify different gene expression between CDK5-knockdown HCT116 cell lines and Scramble HCT116 cell lines.

2016-05-05 | GSE81085 | GEO

Different gene expression between CENPK knockdown and control hepatocellular carcinoma cell line BEL-7404

Project description:We sought to find out the molecular mechanism of CENPK displayed in hepatocellular carcinoma. Microarray experiments were carried out to identify different gene expression between CENPK-knockdown BEL-7404 cell line and Scramble BEL-7404 cell lines.

2018-05-30 | GSE114983 | GEO

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