Trypanosoma brucei strain:RUMP 503
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562204 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10024139_1.fastq.gz | Fastqsanger.gz | |||
| SRR10024139_2.fastq.gz | Fastqsanger.gz | |||
| SRR13858612.fastq.gz | Fastqsanger.gz |
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Project description:Trypanosomes were sorted (0 cells, 1 cell, 50 cells) using a FACSaria III (BD Biosciences; precision: single-cell; nozzle: 100 µm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to gate the cells. Trypanosomes were sorted in 48-wells plate (Brand) filled with 2.6 µL of lysis buffer (0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water). Immediately after sorting cells were placed on ice for 5 minutes and stored at -80 °C. 50 and single trypanosomes were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using one fourth of reagents volumes compared to the supplier instructions. PCR amplification was performed using 26 cycles using supplier recommendations. cDNA was purified using XP beads (Beckman Coulter) and recovered in 15 µL of elution buffer (Takara). Libraries were quantified using the Qubit Hs Assay (Life Technologies) and the qualities of the libraries were further monitored using a Bioanalyzer (Agilent). Similar to what has been published previously 19, 1 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended volumes, 10 minuntes for tagmentation at 55 °C and 1 minute extension time during PCR amplification. Libraries were pooled (96 libraries for NextSeq) and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina's NextSeq 500.
2018-10-09 | GSE120515 | GEO
Project description:Trypanosomes were sorted (1 cell, 10 cells, 50 cells) using a FACSaria III (BD Biosciences; precision: single-cell; nozzle: 100 µm). Forward-scatter area (FCS-A) versus side-scatter area (SSC-A) was used to gate the cells. Trypanosomes were sorted in 48-wells plate (Brand) filled with 2.6 µL of lysis buffer (0.01 µL of RNAse inhibitor (Takara) and 1x Lysis buffer (Takara) in RNAse-free water). Immediately after sorting cells were placed on ice for 5 minutes and stored at -80 °C. 50 and single trypanosomes were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Takara) using one fourth of reagents volumes compared to the supplier instructions. PCR amplification was performed using 26 cycles using supplier recommendations. cDNA was purified using XP beads (Beckman Coulter) and recovered in 15 µL of elution buffer (Takara). Libraries were quantified using the Qubit Hs Assay (Life Technologies) and the qualities of the libraries were further monitored using a Bioanalyzer (Agilent). Similar to what has been published previously 19, 1 ng of cDNA was subjected to a tagmentation-based protocol (Nextera XT, Illumina) using one-quarter of the recommended volumes, 10 minuntes for tagmentation at 55 °C and 1 minute extension time during PCR amplification. Libraries were pooled (96 libraries for NextSeq) and sequencing was performed in paired-end mode for 2 × 75 cycles using Illumina's NextSeq 500.
2018-10-09 | GSE121026 | GEO
Project description:GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes
| PRJNA383843 | ENA
Project description:The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei. Keywords: Trypanosoma, VSG, antigenic switching, HDL-resistance
2007-07-04 | GSE8369 | GEO
Project description:A direct comparison of RNAi in vitro with RNAi in vivo is being performed using RNA interference (RNAi) target sequencing (RIT-Seq) of Trypanosoma brucei to identify all genes specifically required for growth in vivo (the infectome). Assembly of the bloodstream-form T. brucei RNAi library and the RNAi target sequencing (RIT-seq) approach in African trypanosomes were reported previously in Alsford, S. et al. High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res 21, 915-924, 264 doi:gr.115089.110 [pii] 265 10.1101/gr.115089.110 (2011) and Alsford,S et al. High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature 482, 232236 doi:10.1038/nature10771 (2012). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-01-21 | E-ERAD-110 | biostudies-arrayexpress
Project description:African trypanosomes have been recently shown to colonise the skin in a process critical for parasite transmission. However, the tissue responses to infection, especially in the lead to parasite transition from the host skin to the vector remain unresolved. Here, using a combination of spatial and single cell transcriptomics, coupled with imaging mass cytometry and genetic models, we investigated the local immune response of the skin in both a murine model of infection and in human samples from the Democratic Republic of Congo (DRC). Our results provide several novel key findings previously unappreciated in the context of parasitic infections in the skin. Firstly, we identified that the skin stromal cells, in particular interstitial preadipocytes located in the subcutis, upregulate several genes involved in inflammatory signalling and antigen presentation, including several molecules involved in T cell activation and survival. Secondly, we detected a significant expansion of a population of IL-17 producing Vg6 gdT cells in the infected murine skin compared to naïve controls, that occur mainly in the subcutis, that we further validated at the protein level by flow cytometry. In silico cell-cell communication analyses between adipocytes and T cells suggests that adipocytes trigger T cell activation locally via Il6, Il10, and Tnfsf18 signalling, amongst others. Thirdly, mice deficient of Vg6 gdT cells show extensive inflammation, increased IFNg-producing CD4+ T cells, and tissue parasite burden compared to naïve controls, indicating that Vg6 gdT cells are important to limit skin inflammation and parasite replication. Based on these observations, we proposed a model whereby interstitial preadipocytes (and potentially adipocytes) as well as Vg6 gdT cells act concertedly in the subcutis to limit tissue damage and parasite load, thus imposing an immunological barrier for transmission. These studies shed light into the mechanisms of gdT cells-mediated immunity in the skin in the context of African trypanosomes infection, as well as a potential role of immature and mature adipocytes as homeostatic regulators on the skin during chronic infection.
2023-08-08 | GSE226113 | GEO
Project description:The host range of African trypanosomes is influenced by innate protective molecules in the blood of primates. A subfraction of human high-density lipoprotein (HDL) containing apolipoprotein A-I, apolipoprotein L-I, and haptoglobin-related protein is toxic to Trypanosoma brucei brucei but not the human sleeping sickness parasite Trypanosoma brucei rhodesiense. It is thought that T. b. rhodesiense evolved from a T. b. brucei-like ancestor and expresses a defense protein that ablates the antitrypanosomal activity of human HDL. To directly investigate this possibility, we developed an in vitro selection to generate human HDL-resistant T. b. brucei. Here we show that conversion of T. b. brucei from human HDL sensitive to resistant correlates with changes in the expression of the variant surface glycoprotein (VSG) and abolished uptake of the cytotoxic human HDLs. Complete transcriptome analysis of the HDL-susceptible and -resistant trypanosomes confirmed that VSG switching had occurred but failed to reveal the expression of other genes specifically associated with human HDL resistance, including the serum resistance-associated gene (SRA) of T. b. rhodesiense. In addition, we found that while the original active expression site was still utilized, expression of three expression site-associated genes (ESAG) was altered in the HDL-resistant trypanosomes. These findings demonstrate that resistance to human HDLs can be acquired by T. b. brucei. Keywords: Trypanosoma, VSG, antigenic switching, HDL-resistance Bloodstream stages of the Lister strain 427 T. b. brucei (MiTat 1.2), expressing VSG221, were used in these studies. Cells were cultured in HMI-9 medium with the addition of heat inactivated fetal bovine serum (FBS) (10%) and Serum Plus (10%). T. b. brucei 427-221 is an antigenically stable line and contains a single copy of the vsg221 gene within the 221 expression site (221ES). At a cell density of approximately 1,000,000 cells/ml, T. b. brucei 427-221 were exposed to various amounts of human HDLs for 24 h in a 6 well plate. Surviving trypanosomes were counted using a hemocytometer then diluted into fresh HMI-9 medium and allowed to recover for 5-14 days. Once the cells had grown to a density of approximately 1,000,000 cells/ml, they were once again incubated with human HDLs. Each round of selection was performed with increasing concentrations of human HDLs and freezer stocks were prepared for each surviving population. Over nine months we conducted eight rounds of human HDL selection, resulting in a population of T. b. brucei that survived incubation with 800 μl of human HDLs (160 lytic U).
2007-07-04 | E-GEOD-8369 | biostudies-arrayexpress
Project description:ISG65 null trypanosomes were produced to investigate the function of ISG65 in mammalian hosts.
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2021-05-30 | GSE174198 | GEO
Project description:Human African trypanosomiasis, or sleeping sickness, is caused by the protozoan parasite Trypanosoma brucei and induces profound reactivity of glial cells and neuroinflammation when the parasites colonise the central nervous system. However, the transcriptional and functional responses of the brain to chronic T. brucei infection remain poorly understood. By integrating single cell and spatial transcriptomics of the mouse brain, we identified that glial responses triggered by infection are readily detected in the proximity to the circumventricular organs, including the lateral and 3rd ventricle. This coincides with the spatial localisation of both slender and stumpy forms of T. brucei. Furthermore, in silico predictions and functional validations led us to identify a previously unknown crosstalk between homeostatic Cx3cr1+ microglia and Cd138+ plasma cells mediated by IL-10 and B cell activating factor (BAFF) signalling. This study provides important insights and resources to improve understanding of the molecular and cellular responses in the brain during infection with African trypanosomes.
2022-08-29 | GSE200642 | GEO