Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phenotypic activation and repression of three ELAV-like proteins in Trypanosoma brucei

ABSTRACT: Three potential ELAV-like proteins of T. brucei, including Tb927.3.2930, Tb927.7.5380, and Tb927.8.6650, were either inhibited by RNAi or phenotypically activated by over-expression, followed by microarray analysis of the transcriptome. The results indicated that these ELAV-like proteins regulate the abundance of a large number of T. brucei transcripts, potentially through regulation of mRNA stability. Each of the three ELAV-like proteins were either inhibited by RNAi or over-expressed, in stable transgenic procyclic form cell lines. Total RNA was extracted 48h after tetracycline induction of the constructs (except for total RNA from Tb927.8.6650 RNAi which was extracted 24h after tet-induction), and sent to NimbleGen for cDNA synthesis and hybridization. Non-induced cells were analyzed in parallel.

ORGANISM(S): Trypanosoma brucei

SUBMITTER: Hamed Najafabadi

PROVIDER: E-GEOD-46161 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

ATM kinase inhibition in glial cells activates the innate immune response and causes neurodegeneration in Drosophila

Project description:Analysis of the effects of ATM loss on gene expression to identify causes of neurodegeneration. ATM levels were reduced ubiquitously via the temperature-sensitive ATM^8 allele, or via tissue-specific RNAi of ATM (ATMi) using the Gal4/UAS expression system in neurons (Elav-GAL4 and ElavC155-GAL4) or glial cells (Repo-GAL4). A 20-chip study using total RNA representing 2 replicates of 3 control genotypes (ATM^8/+, Repo-GAL4, and ElavC155-GAL4) and 3 experimental genotypes (ATM^8/ATM^8, Repo-ATMi, ElavC155-ATMi), and 4 replicates each of a control (Elav-GAL4) and experimental (Elav-ATMi) genotype

2011-12-10 | E-GEOD-34315 | biostudies-arrayexpress

Characterization of the regulatory programs governed by ELAV-like proteins in Trypanosoma brucei

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-18 | E-GEOD-46162 | biostudies-arrayexpress

Expression analyses of nanos(RNAi) and control(RNAi) Schmidtea mediterranea

Project description:Investigation of whole genome gene expression level changes in nanos(RNAi) Schmidtea mediterranea, compared to control animals. nanos(RNAi) animals are devoid of germ cells The samples analyzed in this study are further described in Wang, Y., Stary, JM., Wilhelm, JE. and Newmark, PA. 2010. A eight chip study using total RNA recovered from asexual nanos(RNAi), asexual control, juvenile sexual nanos(RNAi), and juvenile sexual control animals. Each chip measures the expression level of 16,797 ESTs from S. mediterranea with 10 60-mer probe pairs (PM/MM) per gene, with two-fold technical redundancy.

2010-09-01 | E-GEOD-22797 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24 part 2

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with isothermal probes (hg17) 7 chip study, using 7 independent samples.

2013-04-11 | E-GEOD-45922 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24 part 3

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. 3 chips with 3 arrays each study, using 3 pairs of normal vs. tumor tissue and 3 replicates of the same sample. Each chip contained one pair of normal vs. tumor and one copy of the repeated sample.

2013-04-11 | E-GEOD-45925 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24 part 1

Project description:Investigation on expression levels of normal tissue from prostate cancer patients on locus 8q24. The region chr8:127640000-129120000 is tiled with 60 nt probes at 10 nt interval (hg18) 7 chip study, using 7 independent samples.

2013-04-11 | E-GEOD-45920 | biostudies-arrayexpress

Expression analysis of prostate tissue on locus 8q24

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-11 | E-GEOD-45934 | biostudies-arrayexpress

Nucleosome occupancy changes in mammalian cell differentiation and reprogramming (microarray)

Project description:Embryonic stem cells (ESCs) and induced-pluripotent stem cells (iPSCs) self-renew and differentiate into an array of cell types in vitro and in vivo. A complex network of genetic and epigenetic pathways regulates the self-renewal and differentiation of these pluripotent cells, and the structure and covalent modifications of chromatin play a prominent role in this process. We examine nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach that enabled the identification of regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. The majority of changes in nucleosomal signatures that occur in differentiation are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of pluripotency and likely identify key regulatory regions that play a role in determining cell identity. A six chip study using total RNA recovered from three cell types with 2 replicates each

2014-07-31 | E-GEOD-59061 | biostudies-arrayexpress

The gene expression profiling array of LncRNA between tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma

Project description:Investigation of whole genome gene expression level changes of LncRNAs in tumor tissues and paired non-tumor tissues in HBV-positive hapatocellular carcinoma. The different expression genes were further analysised. The human LncRNA microarray analysis of the 10 samples (5 non-tumor tissues and 5 paired tumor tissues) were completed. Total RNA from each sample was quantified using the NanoDrop ND-1000 and RNA integrity was assessed using standard denaturing agarose gel electrophoresis. Total RNA of each sample was used for labeling and array hybridization as the following steps: 1) Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit; 2) ds-cDNA labeling with NimbleGen one-color DNA labeling kit; 3) Array hybridization using the NimbleGen Hybridization System and followed by washing with the NimbleGen wash buffer kit; 4) Array scanning using the Agilent Scanner G2505C. Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and mRNA level (*_RMA.calls) files were generated after normalization. All mRNAs level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.mRNAs that at least 3 out of 6 samples have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for further data analysis. Differentially expressed mRNAs were identified through Volcano Plot filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Finally, Hierarchical Clustering was performed to show the distinguishable mRNAs expression pattern among samples.

2013-08-10 | E-GEOD-49713 | biostudies-arrayexpress

Comparison of transcriptional profiles of PBMCs from HIV-infected rapid progressors and chronic progressors

Project description:A significant percentage of HIV-infected individuals experience a sharp decline in CD4+ T cell counts and progress to AIDS quickly after primary infection. Identification of biomarkers distinguishing rapid progressors (RPs) versus chronic progressors (CPs) is critical for early clinical intervention and could provide novel strategies to facilitate vaccine design and immune therapy. mRNA and miRNA expression profiles in the peripheral blood mononuclear cells (PBMCs) of RPs and CPs were investigated at 111Â±22 days (MeanÂ±SD) of HIV infection. The association of mRNA and miRNA expression with disease progression was examined by receiver operating characteristic analysis and Kaplan-Meier survival analysis. Pathway enrichment analysis showed that genes with deregulated expression in RPs are primarily involved in apoptosis pathways. Furthermore, we found that 5 miRNAs (miR-31, -200c, -526a, -99a and -503) in RPs were significantly decreased compared to those in CPs (P<0.05). The decreased expression of these miRNAs was associated with rapid disease progression of HIV infection with a 94% predictive value as measured by the area under the curve. The upregulated predicted targets from the 5 signature miRNAs and all upregulated genes identified from mRNA microarray converged to the apoptosis pathway. Moreover, overexpression of miR-31 in primary human T cells promoted their survival. Our results have identified a distinct transcriptomic signature in PBMCs of RPs and provided novel insights to the pathogenesis of HIV infection. A cohort of primary HIV infected individuals with different disease outcome were enrolled in this study. We included 6 individuals with rapid disease progression (RP), seven with chronic disease progression (CP). The HIV infected individuals were never on therapy before the time of sample taken.

2013-05-01 | E-GEOD-44216 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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