Project description:MAK98 strain trypanosomes were cultured for 7 weeks. Control sequences are uploaded separately. These are paired reads in separate files.
Project description:We analysed differentiation of the EATRO1125 strain of Trypanosoma brucei brucei, which was first isolated in 1966 from a bushbuck (Tragelaphus scriptus) in Uganda (origin stated (Bouteillea, 1995) without an original reference.<br>To analyse gene expression, we isolated at least 3 x 10e8 trypanosomes at different differentiation states, using two independent biological replicates. Bloodstream forms were harvested at a density of 2 x 10e5/ml (low density, logarithmic growth), and 2 x 10e6/ml (high density, logarithmic growth). Cells were also taken immediately upon attaining the density of 2 x 106/ml, treated with 3 mM cis-aconitate and moved to a room at 27M-0C. Samples were taken 30 min, 60 min, 12h and 24h after this. At 24 h the cells were centrifuged, resuspended (at 27M-0C) in MEM-Pros medium, which contains proline as the major energy source. Samples were taken again at 48h and 72h. A culture that had been maintained for several weeks after transformation was used as a source of established procyclic trypanosomes.
Project description:Protein coding genes in the trypanosome genome are organized in polycistronic transcription units (PTUs). How RNA Polymerase II (Pol II) initiates PTU transcription has not been resolved and the current model favors initiation driven by chromatin epigenetic marks, rather than core-promoters. Here, we identify sequence-specific core promoters by functional characterization of ChIP-Seq Pol II accumulation-peaks. Sequences located between oppositely orientated PTUs contained two independent and distinct core promoters, driving unidirectional transcription. Detailed analysis of one promoter identified 75 bp, necessary and sufficient to fully drive reporter expression, and containing short functional motifs. Analysis of further promoters suggested activity and initiation is regulated and both, focused and dispersed transcription patterns were found. Thus, in contrast to the model of unregulated and promoter-independent transcription initiation, sequence-specific promoters determine the initiation of RNA Pol II transcription of protein coding genes in trypanosomes. These findings resolve the discrepancy between trypanosomes and other eukaryotes in how Pol II initiates protein-coding gene transcription.
Project description:These are the ribosomal subunit fractions from the polysome gradients. investigating effect of heat shock on procyclic-form trypanosomes.
Project description:Expression analysis was performed with in vitro cultured cerebellar granule neurons (CGNs) isolated from rat brain. The CGNs were culture for four weeks. Each sample was collected after interval of seven days. No treatment was given to any cultured neurons at any time point. The purpose of the experiment was to identify the genes differentially expressed during the senescence of CGNs. The experiment is useful in revealing the senescence associated genetic markers in neurons.