Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Coordinated Progression Through Two Subtranscriptomes Underlies the Tachyzoite Cycle of Toxoplasma gondii

ABSTRACT: We describe the cell cycle transcriptome of the Toxoplasma gondii that has emerged as a major genetic model for the study of Apicomplexa parasites. Two distinct transcriptional waves accompany the relatively simple binary replication of tachyzoite stage (endodyogeny) functionally separating conserved gene expression in the eukaryotic G1 phase from the lineage-specific expression that predominates in the parasite S phase and mitotic periods. This division of transcriptional focus closely mirrors the intimate relationship that has evolved between mitosis and building of the daughter parasites and invasion organelles. Promoter mechanisms appear to orchestrate the induction of gene expression in dividing tachyzoites with up to two dozen cell cycle AP2 factors likely acting within a transcriptional regulatory network to coordinate the parasite cell cycle transcriptome. To characterize the cell cycle transcriptome of Toxoplasma tachyzoites, we expanded a thymidine-synchrony model to isolate sufficient RNA for microarray expression studies. The ToxoGeneChip microarray (http://ancillary.toxodb.org/docs/Array-Tutorial.html) was used to measure mRNA expression in 13 duplicate samples (R0 to R12) covering 12 hours post-synchronization and nearly two tachyzoite replication cycles.

ORGANISM(S): Toxoplasma gondii

SUBMITTER: Michael Behnke

PROVIDER: E-GEOD-19092 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of human primary skin fibroblasts throughout the cell cycle after synchronization by serum starvation or by serum starvation and thymidine blocking

Project description: Not available

2008-01-03 | E-TABM-263 | biostudies-arrayexpress

Cell cycle promoter tiling

Project description:Discover novel transcriptional units upstream of cell cycle genes Transcription of long noncoding RNAs (lncRNAs) within gene regulatory elements can modulate gene activity in response to external stimuli, but the scope and functions of such noncoding transcription are not known. Here we use an ultra-high density array that tiles the promoters of 56 cell cycle genes to interrogate 108 samples representing diverse perturbations. We identify 216 transcribed regions that encode putative lncRNAs--many of which have RT-PCR-validated periodic expression during the cell cycle, show altered expression in human cancers, and are regulated in expression by specific oncogenic stimuli, stem cell differentiation, or DNA damage. 53 samples tiled against respective controls

2011-05-21 | E-GEOD-28631 | biostudies-arrayexpress

Chip-chip from C-33 cells expressing FLAG-HPV1 E2 with FLAG-HPV1 E2

Project description:HPV1 E2 binds with Brd4 to host mitotic chromosomes. To identify the targets, chromatin was prepared from mitotic C-33 cells expressing HPV1 E2, and analyzed by ChIP-chip analysis for binding to a portion of the human genome. E2 and Brd4 bind to active promoters in interphase C-33 cells (Jang et al., 2009), however, in mitosis E2 was observed instead to bind to a few extremely broad peaks on several chromosomes. These peaks ranged in size from several hundred Kb to >1 Mb and, for the most part, overlapped coding regions. Signals of anti-FLAG E2 ChIP DNA from mitotic HPV1 E2 expressing C-33 cells

2014-04-14 | E-GEOD-52312 | biostudies-arrayexpress

Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

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

2013-11-06 | E-GEOD-52100 | biostudies-arrayexpress

Identification of cell cycle-regulated genes periodically expressed in U2OS cells and their regulation by FOXM1 and E2F transcription factors

Project description:We identified the cell cycle-regulated mRNA transcripts genome-wide in the osteosarcoma derived U2OS cell line. This resulted in 2,140 transcripts mapping to 1,871 unique cell cycle-regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identified genomic loci bound by the G2/M transcription factor FOXM1 by Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associated these with cell cycle-regulated genes. FOXM1 was bound to cell cycle-regulated genes with peak expression in both S phase and G2/M phases. ChIP-seq genomic loci were shown to be responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle-transcription factors (E2F1, E2F4, E2F6, and GABPA) from ENCODE and ChIP-seq data for the DREAM complex, found that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle regulated genes in a second cancer derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle. Cell cycle-regulated gene expression identified from three double thymidine time courses and one thymidine nocodazole time course.

2013-10-11 | E-GEOD-50988 | biostudies-arrayexpress

Toxoplasma HCE1 Immunoprecipitations

Project description:IP-MS experiments to identify interacting proteins of Toxoplasma HCE1.

2019-04-05 | PXD012103 | Pride

Toxoplasma MYR1 Immunoprecipitations

Project description:IP-MS experiments to identify interacting proteins of Toxoplasma MYR1.

2020-02-20 | PXD016383 | Pride

Preferential phosphorylation on old histones during early mitosis in human cells

Project description:How histone posttranslational modifications (PTMs) are inherited through cell cycle remains poorly understood. Canonical histones are made in the S phase of cell cycle. Combining mass spectrometry-based technologies and stable isotope labeling by amino acids in cell culture (SILAC), we interrogate the distributions of multiple major histone PTMs on old versus new histones in synchronized human cells. We show that histone PTMs can be grouped to three categories accordingly to their distributions. Most lysine mono-methylation and acetylation PTMs are either symmetrically distributed on old and new histones, or asymmetric on new histones. In contrast, most di- and tri-methylation PTMs are asymmetric on old histones, suggesting the inheritance of different PTMs is regulated distinctly. Intriguingly, old and new histones are distinguished in their phosphorylation status during early mitosis, in three different human cell types: Hela, 293T and human foreskin fibroblast (HFF) cells. The mitotic hallmark H3S10ph is predominantly associated with old H3 at early mitosis and become symmetric with the progression of mitosis. The same distribution pattern is found on other mitotic histone phosphorylation marks, including H3T3/T6ph, H3.1/2S28ph and H1.4S26ph, excluding S28/S31ph on the H3 variant H3.3. Although H3S10ph often associates with the neighboring K9 di- or tri-methylation, they are not required for the asymmetric distribution of S10ph on the same H3 tail. Inhibition of the kinase Aurora B does not change the distribution pattern despite significant reduction of H3S10ph levels. K9me2 abundance on the new H3 is significantly reduced after Aurora B inhibition, suggesting a crosstalk between H3S10ph and H3K9me2.

2016-06-01 | PXD003709 | Pride

Transcription profiling by array of human pluripotent stem cells

Project description:This SuperSeries is composed of the following subset Series: GSE15491: Generation of pluripotent stem cells GSE18147: Dys and Eureprogramming Refer to individual Series

2010-05-27 | E-GEOD-18265 | biostudies-arrayexpress

Dys and Eureprogramming

Project description:Pluripotent stem cells have the potential to differentiate in vitro in many, if not all, functional cell types. Induced pluripotent stem cells (iPS) have recently emerged as a reproducible model of pluripotent stem cells that can be generated from post-natal tissues. To understand this process at the transcriptome level, we generated iPS cell lines, partially reprogrammed cell lines and compared their transcriptome with that of the partental human foreskin fibroblasts and human embryonic stem cell lines. Four categories of samples, comprising human foreskin fibroblasts, fully reprogrammed iPS cell lines, partially reprogrammed iPS cell lines and human embryonic stem cell lines were compared using Significance Analysis of Microarrays (SAM). These data were also compared to a compendium of differentiated human samples and a pluripotency classifier was computed.

2010-05-27 | E-GEOD-18147 | biostudies-arrayexpress

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