GEO DataSets

(Submitter supplied) Targeted gRNA screen against putative nucleic-acid binding proteins in a differentiation reporter strain context. By looking for gRNAs enriched in parasites no longer able to activate reporter expression, we can identify genes essential for this process

Organism:

Toxoplasma gondii

Type:

Other

Platform:

GPL26741

20 Samples

Download data: TXT

(Submitter supplied) Using an epitope-tagged BFD1-complemented strain, the genomic binding of BFD1 was assessed in alkaline-stress induced bradyzoites.

Organism:

Toxoplasma gondii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26741

2 Samples

Download data: BEDGRAPH, NARROWPEAK

(Submitter supplied) WT (ME49∆KU80), ∆BFD1, or ∆BFD1/DD-BFD1-Ty parasites were treated with the stabilizing ligand Shield-1 (all three) or vehicle alone (WT and ∆BFD1/DD-BFD1-Ty) to identify genes differentially regulated by overexpression of BFD1.

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25973

15 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Toxoplasma gondii

Type:

Other; Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

63 Samples

Download data: BEDGRAPH, NARROWPEAK, TXT

(Submitter supplied) Using a differentiation reporter strain, unstressed parasites (tachyzoites) or stressed, reporter positive parasites (bradyzoites) were isolated by flow cytometry and analyzed for differential gene expression.

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16774

10 Samples

Download data: TXT

(Submitter supplied) To profile cell-cycle progression and the asynchronous process of differentiation, we performed single-cell RNA-sequencing (scRNA-Seq) of T. gondii using Seq-Well (Gierahn et al., 2017). Wild-type or ∆BFD1 parasites were grown under unstressed or stressed conditions (24, 48 or 72 h), mechanically released from host cells, and analyzed.

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

16 Samples

Download data: TXT

(Submitter supplied) Toxoplasma gondii persists in humans by converting from actively replicating acute stage tachyzoites to slow-growing chronic stage bradyzoites. The molecular mechanisms that mediate T. gondii differentiation remain poorly understood. Through a chemical mutagenesis screen, we identified translation initiation factor eIF1.2 as being critical for T. gondii differentiation. The presence of an F97L mutation in eIF1.2 identified in the screen or the complete lack eIF1.2 (∆eIF1.2) markedly impeded bradyzoite cyst formation in culture and in the brains of infected mice. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL23466

24 Samples

Download data: TXT

(Submitter supplied) Overexpression of DDHA-AP2IX-9 under a tubulin promoter in type III CTG strain. Differential expression analysis under addition of shield-1 and comparison to the non-bradyzoite induced parental culture revealed a global downregulation of the bradyzoite gene expression program including canonical markers like BAG1.

Organism:

Toxoplasma gondii

Type:

Expression profiling by array

Platform:

GPL16542

11 Samples

Download data: CEL

(Submitter supplied) Toxoplasma gondii, a protozoan parasite, undergoes a complex and poorly understood developmental process that is critical for establishing a chronic infection in its intermediate hosts. Here, we applied single-cell RNA-sequencing (scRNA-seq) on >5,400 Toxoplasma in both tachyzoite and bradyzoite stages using three widely studied strains to construct a comprehensive atlas of cell-cycle and asexual development, revealing hidden states and transcriptional factors associated with each developmental stage. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

8 Samples

Download data: H5

(Submitter supplied) Two forms of the protozoan parasite Toxoplasma gondii are associated with intermediate hosts such as humans: rapidly growing tachyzoites are responsible for acute illness, whereas slowly dividing encysted bradyzoites can remain latent within the tissues for the life of the host. In order to identify genetic factors associated with parasite differentiation, we have used a strong bradyzoite-specific promoter (identified by promoter trapping) to drive the expression of T. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by array

Platform:

GPL2752

8 Samples

Download data

(Submitter supplied) The protozoan pathogen Toxoplasma gondii has the unique ability to develop a chronic infection in the brain of its host. The T. gondii develops cysts within the neurons that are resilient against the host immune response and current therapeutics. The bradyzoite parasites within the cyst have a sugar-protein-rich wall and a slow-replication cycle, allowing them to remain hidden from the host. This intracellular encysted lifestyle of T. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23377

6 Samples

Download data: GTF, TXT

(Submitter supplied) The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome. Prior work identified a single transcription factor (BFD1) that is both necessary and sufficient to establish the chronic-stage program, making it the master regulator of this process. Recently, we found that parasites lacking a CCCH-type zinc finger RNA-binding protein (BFD2) are also unable to produce chronic forms. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

24 Samples

Download data: XLS

(Submitter supplied) The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome and is induced under alkaline stress. We found that parasites lacking the RNA-binding protein BFD2 are unable to produce chronic forms, consistent with a block in this develomental program. To understand how BFD2 facilitates chronic-stage transcriptional reprogramming in T. gondii, we profiled the transcriptomes of both 'wildtype' and BFD2-knockout parasites under alkaline-stressed and standard culture conditions

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

24 Samples

Download data: XLS

(Submitter supplied) The transcription factor BFD1 is the master regulator of the Toxoplasma chronic-stage differentiation program, which is induced under alkaline stress. Prior work indicated that BFD1 transcriptionally activates five other putative RNA- and DNA-binding proteins during differentiation, suggesting potential secondary roles in shaping the Toxoplasma chronic-stage transcriptome. To describe the distinct genetic cohorts controlled by these factors, we generated individual knockdown strains for each candidate using the auxin inducible degron system (TIR1/AID) and examined the transcriptomic effects of their depletion under alkaline stress.

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

28 Samples

Download data: XLS

(Submitter supplied) Differentiation of proliferative acute stages into semi-quiescent chronic stages is key for Toxoplasma gondii persistence within an infected host. During natural infection, chronic stages are almost exclusively found in neurons, and it is well appreciated that neurons support high rates of spontaneous differentiation in cell culture. Recently, we found that parasites lacking the RNA-binding protein BFD2 are unable to produce chronic forms, consistent with a block in this develomental program. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

9 Samples

Download data: XLS

(Submitter supplied) The acute-to-chronic stage transition in Toxoplasma gondii involes a global restructuring of the parasite transcriptome and can be induced by alkaline stress. Prior work identified the master regulator of this process: a MYB-like transcription factor named BFD1 that is specifically induced under stress and is both necessary and sufficient to drive differentiation. Recently, we found that parasites lacking a CCCH-type zinc finger RNA-binding protein (BFD2) are also unable to produce chronic forms due to an inability to robustly express BFD1. more...

Organism:

Toxoplasma gondii

Type:

Other

Platform:

GPL26742

2 Samples

Download data: XLS

(Submitter supplied) There were three primary objectives to the overall experiment. I. Describe the transcriptome of the oocyst through its development beginning with the freshly excreted, unsporulated oocyst at “Day 0” to a fully sporulated and mature oocyst at “Day 10” and including a mid-sporulation timepoint at “Day 4”. II. Compare the transcriptomes of in vitro vs. in vivo derived bradyzoites. III. Compare expression data from three life stages (oocyst, bradyzoite and tachyzoite) from the same parasite isolate, M4, which has been been characterized as a Type II strain.

Organism:

Toxoplasma gondii

Type:

Expression profiling by array

Platform:

GPL16542

14 Samples

Download data: CEL, TXT

(Submitter supplied) Differential gene expression analysis of TgAP2IV-4 knockout parasites in type I RH diCRE (RHCre) and type II Prudku80 (PruQ) genetic background The gene regulatory role for TgAP2IV-4 was evaluated, in vitro, as tachyzoites (pH 7.0) in 8 strains: RHCre-AP2IV-4 floxed; RHCre-delta_ap2IV-4 clones 27 and 30, PSMB794 cosmid complemented RHCre-dAP2IV-4 populations; PruQ-AP2IV-4 floxed; PruQ-delta_ap2IV-4 clones 10 and 34.

Organism:

Toxoplasma gondii

Type:

Expression profiling by array

Platform:

GPL7186

16 Samples

Download data: CEL

(Submitter supplied) The lack of a comprehensive map of transcription start sites in Toxoplasma gondii has impeded advances in decrypting the molecular mechanisms underlying the regulation of gene expression. Genome-wide approaches for mapping transcription initiation have been instrumental in defining the determinants of transcription initiation in a range of model eukaryotes. We used a protocol for 5′-end RNA sequencing, called RAMPAGE, to sequence the 5′-ends of capped mRNA from ME49 and RH tachyzoites, as well as from ME49 bradyzoites. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25973

6 Samples

Download data: BEDGRAPH

(Submitter supplied) Reactivation of toxoplasmosis poses a significant health risk to chronically infected people especially those with compromised immune systems. Molecular studies of reactivation have been difficult due to the lack of accurate models of bradyzoite recrudescence, which initiates disease reactivation. Here, we performed single cell RNA-sequencing (scRNA-seq) on parasite populations that form after bradyzoite infection of two host-cell types: primary mouse astrocytes and human foreskin fibroblasts. more...

Organism:

Toxoplasma gondii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26742

6 Samples

Download data: MTX, TSV