Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

11 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of Cymelarsan resistant and Cymelarsan sensitive strains of Trypanosoma brucei.

ABSTRACT: A drug sensitive stock of T.b.brucei (STIB247) was used to generate a drug resistant strain (247MelCyR), expressing 130-fold increase in resistance to the melaminophenyl arsenical Cymelarsan (MelCy) by subcurative treatment in mice. Expression of the Cymelarsan resistant phenotype was maintained in 247MelCyR following adaptation to procyclic form in vitro culture. Here we have compared the transcriptomes of the STIB247 and 247MelCyR strains from procyclic cell culture, using digital gene expression (DGE) analysis. Digital gene expression analysis was performed on RNA derived from 2 biological replicates each of Cymelarsan resistant (247MelCyR) and Cymelarsan sensitive (STIB 247), T.b.brucei procyclic cell culture.

ORGANISM(S): Trypanosoma brucei brucei

SUBMITTER: Anneli Cooper

PROVIDER: E-GEOD-23288 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Molecular profiling of human mammary gland links breast cancer risk to a p27+ cell population with progenitor characteristics

Project description:Gene expression, DNA and histone methylation profiles were performed on multiple cell types purified from normal human nulliparous and parous breast tissue using SAGE-seq, MSDK-seq and ChIP-seq [GSE26141]. SAGE-seq, MSDK-seq and ChIP-seq libraries were made from individual cell types and integrated to find a comprehensive view of parity associated changes.

2013-06-13 | E-GEOD-32017 | biostudies-arrayexpress

Transcriptome analysis of Cymelarsan resistant and Cymelarsan sensitive strains of Trypanosoma brucei.

Project description:A drug sensitive stock of T.b.brucei (STIB247) was used to generate a drug resistant strain (247MelCyR), expressing 130-fold increase in resistance to the melaminophenyl arsenical Cymelarsan (MelCy) by subcurative treatment in mice. Expression of the Cymelarsan resistant phenotype was maintained in 247MelCyR following adaptation to procyclic form in vitro culture. Here we have compared the transcriptomes of the STIB247 and 247MelCyR strains from procyclic cell culture, using digital gene expression (DGE) analysis.

2011-07-28 | GSE23288 | GEO

Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium [MSDK-Seq]

Project description:Here we describe the application of high-throughput sequencing technology for profiling histone and DNA methylation, and gene expression patterns of normal human mammary progenitor-enriched and luminal lineage-committed cells. We observed significant differences in histone H3 lysine 27 tri-methylation (H3K27me3) enrichment and DNA methylation of genes expressed in a cell type-specific manner, suggesting their regulation by epigenetic mechanisms and a dynamic interplay between the two processes that together define developmental potential. The technologies we developed and the epigenetically regulated genes we identified will accelerate the characterization of primary cell epigenomes and the dissection of human mammary epithelial lineage-commitment and luminal differentiation. Global profiling of differentially methylated regions in 2 cell types from 6 individuals.

2011-03-01 | E-GEOD-26139 | biostudies-arrayexpress

Digital gene expression tag profiling of digit morphologies in bats

Project description:As the only truly flying mammals, bats use their unique wing formed from elongated digits connected by membranes to power their flight. The forelimb of bats consists of four elongated digits (digits II-V) and one shorter digit (digit I) that is morphologically similar to the hindlimb digits. Elongation of bat forelimb digits is thought to results from changes in the temporal and spatial expression of a number of developmental genes. As a result, comparing gene expression profiles between short and elongated digit morphologies of the fore- and hindlimbs may elucidate the molecular mechanisms underlying digit elongation in bats. Here, we performed a large-scale analysis of gene expression of forelimb digit I, forelimb digits II-V, and all five hindlimb digits in Myotis ricketti using digital gene expression tag profiling approach. Results of this study not only implicate several developmental genes as robust candidates underlying digit elongation in bats, but also provide a better understanding of the genes involved in autopodial development in general. A large-scale analysis of gene expression of 3 different parts of autopods in Myotis ricketti using digital gene expression tag profiling approach.

2010-12-06 | E-GEOD-20038 | biostudies-arrayexpress

Transcriptome analysis of two life cycle stages of Trypanosoma brucei gambiense

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. 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.

2010-07-21 | E-GEOD-18065 | biostudies-arrayexpress

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using Next Generation Sequencing

Project description:We established a protocol of the SuperSAGE technology combined with next-generation sequencing, coined “High-Throughput (HT-) SuperSAGE”. SuperSAGE is a method of digital gene expression profiling that allows isolation of 26-bp tag fragments from expressed transcripts. In the present protocol, index (barcode) sequences are employed to discriminate tags from different samples. Such barcodes permit to enable researchers to analyze digital tags from many transcriptomes of many samples in a single sequencing run by simply pooling the libraries. Here, we demonstrated that HT-SuperSAGE provided highly sensitive, reproducible and accurate digital gene expression data. By increasing throughput for analysis in HT-SuperSAGE, various applications were expected and several examples of its applications were introduced in the present study, including analyses of laser-microdissected cells, biological replicates or tag extraction using different anchoring enzymes. 27 different tissue samples from three different life organisms were analyzed. About 2 samples, three different anchoring enzymes were employed.

2010-09-30 | E-GEOD-20682 | biostudies-arrayexpress

Transcriptome analysis of two life cycle stages of Trypanosoma brucei gambiense

2010-07-22 | GSE18065 | GEO

Global transcriptional profiling of oleaginous yeast Rhodosporidium toruloides under nitrogen limitation.

Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples. Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)

2012-06-29 | E-GEOD-39023 | biostudies-arrayexpress

Digital gene expression (DGE) of PaWB phytoplasma-infected Paulownia witches

Project description:Here we performed a transcriptomic study on PaWB phytoplasma-infected Paulownia sp. using Solexa/IlluminaM-bM-^@M-^Ys high-throughput digital gene expression (DGE) system. 4 DGE libraries (from 2 virus-infected samples and 2 healthy samples) were constructed, and the gene expression variations between the PaWB phytoplasma-infected (diseased) sample and the corresponding healthy sample were compared. Thousands of differentially expressed genes were obtained by the comparison, and KEGG pathway analysis of these genes suggested that many biological processes were responded to PaWB infection. To investigate the response of Paulownia sp. to PaWB infection, we collected four samples in two groups, namely the tissue cultured group (containing healthy sample TH and diseased sample TD) and field-grown group (containing healthy sample FH and diseased sample FD). Four individual tag libraries from these samples were constructed in parallel. For the gene expression analysis, the digital gene expression (DGE) data of diseased sample were compared to that of healthy sample in each group to obtain the gene expression variations.

2014-10-01 | E-GEOD-42087 | biostudies-arrayexpress

Digital gene and expression profiling of primary acute lymphoblastic leukemia (ALL) cells

Project description:This SuperSeries is composed of the following subset Series: GSE26530: Digital gene expression profiling of primary acute lymphoblastic leukemia cells GSE26865: Gene expression profiling of primary acute lymphoblastic leukemia (ALL) cells Refer to individual Series

2011-12-20 | E-GEOD-26878 | 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