Entamoeba plus Caco2 cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Entamoeba histolytica
PROVIDER: GSE2979 | GEO | 2005/07/22
SECONDARY ACCESSION(S): PRJNA104775
REPOSITORIES: GEO
Similar Datasets
Project description:Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses. Using a genomic DNA microarray consisting of 1.6 - 2.0 kb genomic inserts we have generated a transcriptional profile of 1,971 unique parasite transcripts. The arrays in this experiment set were used to (1) estimate relative transcript abundance for Entamoeba histolytica (HM-1:IMSS) trophozoites in mid-logarithmic growth and (2) to examine changes in the transcriptional profile of Entamoeba histolytica when the parasite interacts with colonic epithelial cells (Caco-2). A time course was used such that RNA was isolated from ameba alone and ameba + Caco-2 cells at 3hrs, 6hrs and 9hrs corresponding to 10%, 50% and 90% cell monolayer destruction. At least two biological experiments and three replicates were used for each time point. Groups of assays that are related as part of a time series. User Defined
2005-07-22 | E-GEOD-2979 | biostudies-arrayexpress
Project description:Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses. Using a genomic DNA microarray consisting of 1.6 - 2.0 kb genomic inserts we have generated a transcriptional profile of 1,971 unique parasite transcripts. The arrays in this experiment set were used to examine changes in the transcriptional profile of Entamoeba histolytica when the parasite interacts with colonic epithelial cells (Caco-2). A time course was used such that RNA was isolated from ameba alone and ameba + Caco-2 cells at 3hrs, 6hrs and 9hrs corresponding to 10%, 50% and 90% cell monolayer destruction. At least two biological experiments and three replicates were used for each time point.
2005-07-06 | E-SMDB-3208 | biostudies-arrayexpress
Project description:Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses. Using a genomic DNA microarray consisting of 1.6 - 2.0 kb genomic inserts we have generated a transcriptional profile of 1,971 unique parasite transcripts. The 12 arrays in this experiment set were used to estimate relative transcript abundance for Entamoeba histolytica (HM-1:IMSS) trophozoites in mid-logarithmic growth.
2005-07-06 | E-SMDB-3205 | biostudies-arrayexpress
Project description:Entamoeba histolytica is a protozoan parasite that causes colitis and liver abscesses. Several Entamoeba species and strains with differing levels of virulence have been identified. E. histolytica HM-1:IMSS is a virulent strain, E. histolytica Rahman is a nonvirulent strain, and Entamoeba dispar is a nonvirulent species. We used an E. histolytica DNA microarray consisting of 2,110 genes to assess the transcriptional differences between these species/strains with the goal of identifying genes whose expression correlated with a virulence phenotype. We found 415 genes expressed at lower levels in E. dispar and 32 genes with lower expression in E. histolytica Rahman than in E. histolytica HM-1:IMSS. Overall, 29 genes had decreased expression in both the nonvirulent species/strains than the virulent E. histolytica HM-1:IMSS. Interestingly, a number of genes with potential roles in stress response and virulence had decreased expression in either one or both nonvirulent Entamoeba species/strains. These included genes encoding Fe hydrogenase (9.m00419), peroxiredoxin (176.m00112), type A flavoprotein (6.m00467), lysozyme (6.m00454), sphingomyelinase C (29.m00231), and a hypothetical protein with homology to both a Plasmodium sporozoite threonine-asparagine-rich protein (STARP) and a streptococcal hemagglutinin (238.m00054). The function of these genes in Entamoeba and their specific roles in parasite virulence need to be determined. We also found that a number of the non-long-terminal-repeat retrotransposons (EhLINEs and EhSINEs), which have been shown to modulate gene expression and genomic evolution, had lower expression in the nonvirulent species/strains than in E. histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence. A species experiment design type assays differences between distinct species. Keywords: species_design
2006-02-02 | GSE4139 | GEO
Project description:Entamoeba histolytica is a protozoan parasite that causes colitis and liver abscesses. Several Entamoeba species and strains with differing levels of virulence have been identified. E. histolytica HM-1:IMSS is a virulent strain, E. histolytica Rahman is a nonvirulent strain, and Entamoeba dispar is a nonvirulent species. We used an E. histolytica DNA microarray consisting of 2,110 genes to assess the transcriptional differences between these species/strains with the goal of identifying genes whose expression correlated with a virulence phenotype. We found 415 genes expressed at lower levels in E. dispar and 32 genes with lower expression in E. histolytica Rahman than in E. histolytica HM-1:IMSS. Overall, 29 genes had decreased expression in both the nonvirulent species/strains than the virulent E. histolytica HM-1:IMSS. Interestingly, a number of genes with potential roles in stress response and virulence had decreased expression in either one or both nonvirulent Entamoeba species/strains. These included genes encoding Fe hydrogenase (9.m00419), peroxiredoxin (176.m00112), type A flavoprotein (6.m00467), lysozyme (6.m00454), sphingomyelinase C (29.m00231), and a hypothetical protein with homology to both a Plasmodium sporozoite threonine-asparagine-rich protein (STARP) and a streptococcal hemagglutinin (238.m00054). The function of these genes in Entamoeba and their specific roles in parasite virulence need to be determined. We also found that a number of the non-long-terminal-repeat retrotransposons (EhLINEs and EhSINEs), which have been shown to modulate gene expression and genomic evolution, had lower expression in the nonvirulent species/strains than in E. histolytica HM-1:IMSS. Our results, identifying expression profiles and patterns indicative of a virulence phenotype, may be useful in characterizing the transcriptional framework of virulence.
2006-01-03 | E-SMDB-3589 | biostudies-arrayexpress
Project description:We examined the stress response in Entamoeba histolytica trophozoites by comparing untreated log-phase HM-1:IMSS trophozoites to those subjected to heat shock at 42C for 1 hour. Keywords: stress reponse
2007-03-01 | GSE6650 | GEO
Project description:Up until now, the existence of Dnmt2-mediated DNA methylation has mostly been supported by focal analyses in organisms that contain Dnmt2, but no Dnmt1 or Dnmt3 DNA methyltransferase. In these organisms, several independent studies have also provided support for a biologically important function of Dnmt2-dependent DNA methylation. For example, Dnmt2-dependent methylation in Entamoeba histolytica, the causative agent of amebic dysentery, has been connected to the parasite s virulence. However, global DNA methylation levels in Entamoeba have been found to be very low. In addition, no specific features, such as CpG-specificity and specificity for certain genetic subcompartments have been described. This distinguishes Dnmt2-dependent methylation patterns from all other known methylomes and has raised questions about the validity of the underlying results. We have used whole-genome bisulfite sequencing for an unbiased characterization of the Entamoeba histolytica methylome at single-base resolution in a E.histolytica strain HM-1:IMSS devoid of significant level of EhDnmt2 (Ehmeth) expression.
2011-08-10 | GSE31295 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE2978: Entamoeba heat shock experiments GSE2979: Entamoeba plus Caco2 cells Abstract: We have developed an Entamoeba histolytica genomic DNA microarray and used it to develop a transcriptional profile of 1,971 E. histolytica (HM-1:IMSS) genes. The arrays accurately detected message abundance and 31-47% of amebic genes were expressed under standard tissue culture conditions (levels detectable by Northern blot analysis or RT-PCR respectively). Genes expressed at high levels ( approximately 2% of total) included actin (8.m00351), and ribosomal genes (20.m00312). Moderately expressed genes ( approximately 14% of total) included cysteine proteinase (191.m00117), profilin (156.m00098), and an Argonaute family member (11.m00378). Genes with low-level expression ( approximately 15% of total) included Ariel1 (160.m00087). Genes with very low expression ( approximately 16% of total) and those not expressed ( approximately 52% of total) included encystation-specific genes such as Jacob cyst wall glycoprotein (33.m00261), chitin synthase (3.m00544), and chitinase (22.m00311). Transcriptional modulation could be detected using the arrays with 17% of genes upregulated at least two-fold in response to heat shock. These included heat shock proteins (119.m00119 and 279.m00091), cyst wall glycoprotein Jacob (33.m00261), and ubiquitin-associated proteins (16.m00343; 195.m00092). Using Caco-2 cells to model the host-parasite interaction, we verified that host cell killing was dependent on live ameba. However, surprisingly these events did not appear to induce major transcriptional changes in the parasites. Refer to individual Series
2006-03-07 | E-GEOD-4400 | biostudies-arrayexpress
Project description:Entamoeba histolytica is a protozoan parasite which causes colitis and liver abscesses. A pilot microarray consisting of 360 unique parasite genes was constructed using identical methods to the larger array (1,971 unique genes). The four arrays in this data set were used to ascertain whether the microarrays would be useful in detecting changes in transcript abundance by exposing parasites to heat shock (42 0C for 1 hr). Approximately, 17% of the genes were regulated by at least two fold including many genes previously shown to be involved in heat shock response. This data confirmed that the genomic DNA arrays were useful in detecting changes in transcript abundance.
2005-07-06 | E-SMDB-3207 | biostudies-arrayexpress
Project description:Up until now, the existence of Dnmt2-mediated DNA methylation has mostly been supported by focal analyses in organisms that contain Dnmt2, but no Dnmt1 or Dnmt3 DNA methyltransferase. In these organisms, several independent studies have also provided support for a biologically important function of Dnmt2-dependent DNA methylation. For example, Dnmt2-dependent methylation in Entamoeba histolytica, the causative agent of amebic dysentery, has been connected to the parasite s virulence. However, global DNA methylation levels in Entamoeba have been found to be very low. In addition, no specific features, such as CpG-specificity and specificity for certain genetic subcompartments have been described. This distinguishes Dnmt2-dependent methylation patterns from all other known methylomes and has raised questions about the validity of the underlying results. We have used whole-genome bisulfite sequencing for an unbiased characterization of the Entamoeba histolytica methylome at single-base resolution in a E.histolytica strain HM-1:IMSS devoid of significant level of EhDnmt2 (Ehmeth) expression. Paired-end BS-sequencing was performed on an Illumina Genome Analyzer with read lengths of 105 base pairs and an average insert size of 200 bp.
2011-08-10 | E-GEOD-31295 | biostudies-arrayexpress