GEO DataSets

(Submitter supplied) The study investigates the epigenetic role of G-quadruplexes (G4s) in the differentiation of Trypanosoma brucei brucei, specifically between its bloodstream form (BF) and procyclic form (PC). An in silico analysis identified 115,126 potential G4 sequences (PQSs) across the genome, with 63% having a high probability of G4 formation. These PQSs are unevenly distributed, with notable enrichment in regions associated with antigenic variation, such as variant surface glycoproteins and bloodstream expression sites. more...

Organism:

Trypanosoma brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34844

16 Samples

Download data: COUNTS

(Submitter supplied) In vitro selection of Bloodstream form T. brucei with the trypanosome lytci factor (TLF) led to generation of parasites resistant to TLF. We not show that resistance is due to silencing Pol II transcription initiaiton at promoter for the gene array that includes the TLF receptor gene HpHbR. Reversable transcriptional silencing of the HpHbR gene array and the adjacent gene array, correlates with DNA base J modification of the shared promoter region. more...

Organism:

Trypanosoma brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33832

9 Samples

Download data: TXT

(Submitter supplied) In this work, we examine the function of DRBD18 in T. brucei, here using single cell RNA sequencing (scRNAseq) of uninduced and induced DRBD18 knockdowns. In insect procyclic form, we identified one major and one minor population of cells that dramatically increased upon DRBD18 knockdown. Both of these cell populations were significantly enriched for transcripts that are normally upregulated in the quiescent stumpy bloodstream form and metacyclic (MF) life cycle stages, consistent with a role for DRBD18 in life cycle progression. more...

Organism:

Trypanosoma brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33832

4 Samples

Download data: MTX, TSV

(Submitter supplied) Base J is a modified DNA base that is enriched at RNA polymerase II termination sites. We previously found that base J functions to prevent readthrough transcription within gene clusters via the PJW/PP1 complex. Analysis of the complex in T. brucei faild to identify the catalytic PP1 component. We now show the RNAi ablation of PP1-1 in T. brucei leads to readthrough transcription and expression of downstream genes.

Organism:

Trypanosoma brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33832

12 Samples

Download data: WIG

(Submitter supplied) In this study we combined small RNA isolation from post-ribosomal supernatant with RibOxi-seq to identify 2’-O-methylation (Nm) in single nucleotide resolution. Our analysis identified ~49 Nm sites in tRNA, snRNAs, snoRNAs, 7SL RNA and vtRNA.

Organism:

Trypanosoma brucei brucei TREU927

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL30921

4 Samples

Download data: CSV

(Submitter supplied) In this study we used RibOxi-seq to identify 2’-O-methylation (Nm) present on mRNAs in single nucleotide resolution. Our analysis identified hundreds of Nm sites in mRNAs, predominantly in CDS and 3’ UTR.

Organism:

Trypanosoma brucei

Type:

Other

Platform:

GPL20572

3 Samples

Download data: CSV

(Submitter supplied) Trypanosoma brucei are protozoan parasites that cause sleeping sickness in humans and nagana in cattle. Inside the mammalian host, a quorum sensing-like mechanism coordinates its differentiation from a slender replicative form into a quiescent stumpy form, limiting growth and virulence. SUMOylation is a reversible post-translational modification that enables dynamic regulation of cellular metabolism by the attachment of SUMO monomer or SUMO polymeric chains. more...

Organism:

Trypanosoma brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20572

4 Samples

Download data: XLS

(Submitter supplied) Universal Minicircle Sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich UMS sequence, conserved at the replication origins of minicircles in the kinetoplast DNA, the mitochondrial genome of trypanosomatids. Trypanosoma brucei UMSBP2 has been recently shown to colocalize with telomeres and play an essential role in chromosome ends protection. Here we report that TbUMSBP2 decondenses in vitro DNA molecules, which were condensed by core histones H2B, H4 or linker histone H1. more...

Organism:

Trypanosoma brucei brucei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27986

6 Samples

Download data: NARROWPEAK

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

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL22141

7 Samples

Download data

(Submitter supplied) Depletion of ZC3H41 has minor effects on the transcriptome of procyclic trypanosomes. In general, ZC3H41-regulated transcripts seem to be expressed at low abundance, and almost half of them (43%) are probably non-coding, since the corresponding encoded proteins have not been detected in proteomic surveys . A transcript encoding a trans-sialidase (Tb927.11.11410) was clearly upregulated in ZC3H41-depleted cells .

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22141

3 Samples

Download data: TSV

(Submitter supplied) Data were analyzed with the peak caller MACS2, which gave us a list of 104 mRNAs highly likely to be associated with the complex. There was a notable abundance of mRNAs encoding ribosomal proteins among these top-ranked transcripts (72 of 104 transcripts).

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL22141

4 Samples

Download data: TSV

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

Organism:

Trypanosoma brucei brucei

Type:

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

Platforms:

GPL24992 GPL27986

12 Samples

Download data

(Submitter supplied) This study examines differential expression upon TbSAC3 depletion in Trypanosoma brucei brucei strain 29.13

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21682

6 Samples

Download data: TXT

(Submitter supplied) Trypanosoma brucei is a protozoan parasite that causes human African trypanosomiasis. Its major surface antigen VSG is expressed from subtelomeric loci in a strictly monoallelic manner. We previously showed that the telomere protein TbRAP1 binds dsDNA through its 737RKRRR741 patch to silence VSGs globally. How TbRAP1 permits transcription of the single active VSG is unknown. Through NMR structural analysis, we unexpectedly identify an RNA Recognition Motif (RRM) in TbRAP1, which is unprecedented for RAP1 homologs. more...

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27986

11 Samples

Download data: XLSX

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

Organism:

Trypanosoma brucei brucei

Type:

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

Platform:

GPL22141

19 Samples

Download data: BW

(Submitter supplied) RBP33 depletion results in the overexpression of 40% (bloodstream) or 20% (procyclic) of all transcripts annotated in the 427 2018 genome

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22141

12 Samples

Download data: TSV

(Submitter supplied) Depletion of RBP33 by RNAi does not seem to have profound effects on chromatin accesibility

Organism:

Trypanosoma brucei brucei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22141

7 Samples

Download data: BW

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

Organism:

Trypanosoma brucei brucei

Type:

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

Platforms:

GPL24992 GPL32472

64 Samples

Download data: BW

(Submitter supplied) Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here we report that SET27 and CRD1 together with four biologically novel constituents form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. more...

Organism:

Trypanosoma brucei brucei

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL32472 GPL24992

52 Samples

Download data: BW

(Submitter supplied) Kinetoplastids are a highly divergent lineage of eukaryotes with unusual mechanisms for regulating gene expression. We previously surveyed 65 putative chromatin factors in the kinetoplastid Trypanosoma brucei. Our analyses revealed that the predicted histone methyltransferase SET27 and the Chromodomain protein CRD1 are tightly concentrated at RNAPII transcription start regions (TSRs). Here we report that SET27 and CRD1 together with four biologically novel constituents form the SET27 promoter-associated regulatory complex (SPARC), which is specifically enriched at TSRs. more...

Organism:

Trypanosoma brucei brucei

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL32472 GPL24992

12 Samples

Download data: BW