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ABSTRACT:
PROVIDER: PRJNA735576 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tetrahymena thermophila SB210 micronuclear genome sequencing
| PRJNA51571 | ENA
Project description:In the germline nucleus of Tetrahymena and other ciliates there occurs a peculiar burst of transcriptional activity during sexual reproduction. A major part of the genome is transcribed into noncoding RNA (ncRNA). This ncRNA serves to spot transposable elements (TEs) and other unwanted DNA sequences and marks them for elimination from the soma of the progeny. ncRNA transcription is remarkable for its extent, its occurrence in a nucleus that bears heterochromatic marks and is incapable of transcribing mRNAs and for its concomitance with meiotic DNA recombination. Here we report two novel factors (Emit1 and Emit2) that promote the micronuclear localization of the transcription Mediator complex to allow this unconventional transcriptional program to occur. Another factor (Rib1) may enhance the transcription activity to TE-rich pericentromeric and telomeric regions. The purpose of the LC-MS/MS analysis of Emit1, Emit2 and Rib1 immunoprecipitation samples is to identify their potential interacting partner proteins.
2019-07-11 | PXD012372 | Pride
Project description:Here we report that soon after mating of Oxytricha trifallax, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these 27nt RNAs from various times after mating. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that this 27nt RNA class derives from the parental macronucleus, not the developing macronucleus. These small RNAs are produced equally from both strands of macronuclear nanochromosomes, but in a highly non-uniform distribution along the length of the nanochromosome, and with a particular depletion in the 30 nt telomere-proximal positions. Unlike the Tetrahymena scanRNAs, the Oxytricha macronuclear-derived 27mers are not modified by 2'O-methylation at their 3' ends. Examination of small RNAs produced in Oxytricha trifallax during vegetative growth and at various timepoints during the mating process
2012-04-19 | E-GEOD-37390 | biostudies-arrayexpress
Project description:Tetrahymena thermophila SB210 micronuclear genome sequencing and assembly using long reads
| PRJNA565159 | ENA
Project description:Here we report that soon after mating of Oxytricha trifallax, abundant 27nt small RNAs are produced that are not present prior to mating. We performed next generation sequencing of these 27nt RNAs from various times after mating. Using sequence comparisons between macronuclear and micronuclear versions of genes, we found that this 27nt RNA class derives from the parental macronucleus, not the developing macronucleus. These small RNAs are produced equally from both strands of macronuclear nanochromosomes, but in a highly non-uniform distribution along the length of the nanochromosome, and with a particular depletion in the 30 nt telomere-proximal positions. Unlike the Tetrahymena scanRNAs, the Oxytricha macronuclear-derived 27mers are not modified by 2'O-methylation at their 3' ends.
2012-04-19 | GSE37390 | GEO
Project description:Meiosis occurs in all sexually reproducing unicellular and multicellular eukaryotes. Bouquet formation is indispensible for homologous pairing or recombination during meiotic prophase I, but the regulatory mechanism of this process remain largely unknown. Cyclins regulate the precise meiosis progression by activating cyclin-dependent kinases. We therefore investigated the functional contribution of cyclin Cyc2p during bouquet (named crescent in Tetrahymena) formation in Tetrahymena thermophila. As a conjugation specific gene, CYC2 expression is significantly upregulated at 2-4 h after the initiation of conjugation and Cyc2p mainly localized in cytoplasm as well as weakly in the meiotic micronucleus (Mic). CYC2 knockout mutants failed to form elongated crescent structure and aborted meiotic development. Mic DNA double-strand breakage (DSB) decreased in ΔCYC2 cells as shown by γ-H2A.X staining, consistent with the finding that expression level of SPO11, DMC1, and RAD51 decreased in ΔCYC2 cells. However, ΔCYC2 cells failed to form crescent structure when artificial DSBs were induced, indicating that the inability to enter crescent phase was not completely due to the lack of DSBs. The localization of tubulin showed that impaired structure of nuclei and nuclear membrane may contribute to the blocked Mic elongation. This is further supported by the observation that expression levels of two microtubule associated kinesin genes, KIN11 and KIN141, were significantly downregulated in ΔCYC2 cells. Interestingly, scnRNA accumulation seemed intact in ΔCYC2 cells whereas the intensity of the heterochromatin marker H3K23me3 was abnormally increased. Together, these results showed that cyclin Cyc2p is required for micronuclear meiosis by controlling meiotic prophase chromosome breakage and the microtubule movement of nuclei in Tetrahymena.
2018-12-14 | GSE108064 | GEO
Project description:Comparison of published protocol (Abud et al. Neuron 2016) to simplified method of microglial differentiation which does not require hypoxia or FACS. We show each method produced highly similar microglia.
2018-12-05 | GSE117829 | GEO
Project description:High throughput sequencing is frequently used to discover the location of regulatory interactions on chromatin. However, techniques that enrich DNA where regulatory activity takes place, such as chromatin immunoprecipitation (ChIP), often yield less DNA than optimal for sequencing library preparation. Existing protocols for picogram-scale libraries require concomitant fragmentation of DNA, pre-amplification, or long overnight steps. We report a simple and fast library construction method that produces libraries from sub-nanogram quantities of DNA. This protocol yields conventional libraries with barcodes suitable for multiplexed sample analysis on the Illumina platform. We demonstrate the utility of this method by constructing a ChIP-seq library from 100 pg of ChIP DNA that demonstrates equivalent genomic coverage of target regions to a library produced from a larger scale experiment. Application of this method allows whole genome studies from samples where material or yields are limiting. Comparison of ChIP-seq libraries constructed from 100 pg DNA (this study) and nanograms of DNA (modENCODE). ChIP antibody: H3K27me3, Active Motif 31955.
2013-07-01 | E-GEOD-48431 | biostudies-arrayexpress
Project description:We report novel single-cell RNA-Seq, called Quartz-Seq. Quartz-Seq was simplified method compared with previous methods based on poly-A tailing reaction.
2013-04-04 | GSE42268 | GEO