RNAi of XAC1 (Tb927.7.2780) in Trypanosoma brucei bloodstream forms
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Trypanosoma brucei
SUBMITTER: 
Christine Clayton
PROVIDER: E-MTAB-6239 | ArrayExpress | 2017-12-16
SECONDARY ACCESSION(S): ERP105583
REPOSITORIES: ArrayExpress, ENA
Similar Datasets
Project description:PUF3 was depleted by RNAi for 24h in bloodstream-form trypanosomes (Trypanosoma brucei). No effect was seen on the transcriptome.
2019-06-30 | E-MTAB-8062 | ArrayExpress
Project description:RNAi of XAC1 (Tb927.7.2780) in Trypanosoma brucei bloodstream forms
| PRJEB23805 | ENA
Project description:Achcar2012 - Glycolysis in bloodstream form T. brucei
Kinetic models of metabolism require quantitative knowledge of detailed kinetic parameters. However, the knowledge about these parameters is often uncertain. An analysis of the effect of parameter uncertainties on a particularly well defined example of a quantitative metablic model, the model of glycolysis in bloodstream form Trypanosoma brucei
, has been presented here.
This model is described in the article:
Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism.
Achcar F, Kerkhoven EJ; SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R.
PLoS Comput Biol. 2012 Jan; 8(1):e1002352.
Abstract:
Kinetic models of metabolism require detailed knowledge of kinetic parameters. However, due to measurement errors or lack of data this knowledge is often uncertain. The model of glycolysis in the parasitic protozoan Trypanosoma brucei is a particularly well analysed example of a quantitative metabolic model, but so far it has been studied with a fixed set of parameters only. Here we evaluate the effect of parameter uncertainty. In order to define probability distributions for each parameter, information about the experimental sources and confidence intervals for all parameters were collected. We created a wiki-based website dedicated to the detailed documentation of this information: the SilicoTryp wiki (http://silicotryp.ibls.gla.ac.uk/wiki/Glycolysis). Using information collected in the wiki, we then assigned probability distributions to all parameters of the model. This allowed us to sample sets of alternative models, accurately representing our degree of uncertainty. Some properties of the model, such as the repartition of the glycolytic flux between the glycerol and pyruvate producing branches, are robust to these uncertainties. However, our analysis also allowed us to identify fragilities of the model leading to the accumulation of 3-phosphoglycerate and/or pyruvate. The analysis of the control coefficients revealed the importance of taking into account the uncertainties about the parameters, as the ranking of the reactions can be greatly affected. This work will now form the basis for a comprehensive Bayesian analysis and extension of the model considering alternative topologies.
This model is hosted on BioModels Database
and identified by: MODEL1209130000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
2012-11-20 | BIOMD0000000428 | BioModels
Project description:ZC3H5 was knocked down in bloodstream form T.brucei by RNAi for 0h and 12h. WT bloodstream form cells were used as control. Polysome fractionation was performed, RNA was purified from each fraction and fractions were pooled the following: F=free fraction; M=monosomes; L=light polysomes; H=heavy polysomes. RNA was depleted and RNA-Seq was performed.
2019-06-28 | E-MTAB-8069 | ArrayExpress
Project description:Cy3 and Cy5 direct labelled RNA from Bloodstream MiTat1.1 trypanosomes and Procyclic 427 Lister were hybridized onto JCVI Trypanosoma brucei oligoarrays (version2). Procyclic RNA were used as control for data analysis.
2010-01-01 | E-MEXP-2028 | ArrayExpress
Project description:A direct comparison of RNAi in vitro with RNAi in vivo is being performed using RNA interference (RNAi) target sequencing (RIT-Seq) of Trypanosoma brucei to identify all genes specifically required for growth in vivo (the infectome). Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach in African trypanosomes were reported previously in Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011) and Alsford,S et al. High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 482, 232236 doi:10.1038/nature10771 (2012). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-01-21 | E-ERAD-110 | ArrayExpress
Project description:To look at differential expression of membrane-trafficking genes, <br>we extracted RNA from exponentially growing cultures of T. brucei <br>bloodstream (BSF) and procyclic (PCF) forms, labelled and competitively <br>hybridised the cDNA to the microarray. 8 arrays, representing <br>6 BSF and 5 PCF biological replicates, as well as dye swaps were used.
2008-06-26 | E-MEXP-1529 | ArrayExpress
Project description:Trypanosoma brucei gambiense is the causative agent of the fatal human disease African sleeping sickness. Here we have compared the transcriptome of two different life cycle stages, the potentially human-infective bloodstream form and the non-human-infective procyclic stage, using digital gene expression (DGE) analysis. Overall design: Digital gene expression analysis was performed on RNA from 3 biological replicates of bloodstream cultured T.b. gambiense strain STIB 386 and compared to that from 3 biological replicates of procyclic cultured T.b. gambiense strain STIB 386.
2010-07-22 | GSE18065 | GEO
Project description:The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei. Keywords: Trypanosoma, VSG, antigenic switching, HDL-resistance Overall design: Bloodstream stages of the Lister strain 427 T. b. brucei (MiTat 1.2), expressing VSG221, were used in these studies. Cells were cultured in HMI-9 medium with the addition of heat inactivated fetal bovine serum (FBS) (10%) and Serum Plus (10%). T. b. brucei 427-221 is an antigenically stable line and contains a single copy of the vsg221 gene within the 221 expression site (221ES). At a cell density of approximately 1,000,000 cells/ml, T. b. brucei 427-221 were exposed to various amounts of human HDLs for 24 h in a 6 well plate. Surviving trypanosomes were counted using a hemocytometer then diluted into fresh HMI-9 medium and allowed to recover for 5-14 days. Once the cells had grown to a density of approximately 1,000,000 cells/ml, they were once again incubated with human HDLs. Each round of selection was performed with increasing concentrations of human HDLs and freezer stocks were prepared for each surviving population. Over nine months we conducted eight rounds of human HDL selection, resulting in a population of T. b. brucei that survived incubation with 800 µl of human HDLs (160 lytic U).
2007-07-04 | GSE8369 | GEO
Project description:Surface-exposed proteins of the bloodstream and procyclic forms of T. brucei were biotinylated, affinity purified using streptavidin, and analyzed by LC-MS/MS
2015-03-17 | MSV000079080 | Massive