UV laser-induced, time-resolved transcriptome resonses of Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA530926 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We report changes in the S. cerevisiae transcriptome in response to 30s irradiation with a UV laser
2019-06-18 | GSE129319 | GEO
Project description:Genome-wide mapping of transcription factor binding is generally performed by chemical protein-DNA crosslinking, followed by chromatin immunoprecipitation and deep sequencing (ChIP-seq). Here we present the ChIP-seq technique based on photochemical crosslinking of protein-DNA interactions by high-intensity ultraviolet (UV) laser irradiation in living mammalian cells (UV-ChIP-seq). UV laser irradiation induces efficient and instant formation of covalent “zero-length” crosslinks exclusively between nucleic acids and proteins that are in immediate contact, thus resulting in a “snapshot” of direct protein-DNA interactions in their natural environment. We applied UV-ChIP-seq for genome-wide profiling of the sequence-specific transcriptional repressor B-cell lymphoma 6 (BCL6) in human diffuse large B-cell lymphoma (DLBCL) cells. Our approach resulted in sensitive and precise protein-DNA binding profiles, highly enriched in canonical BCL6 DNA sequence motifs. UV-ChIP-seq also revealed numerous previously undetectable BCL6 binding sites, particularly in more condensed, inaccessible areas of chromatin.
2017-11-06 | GSE103125 | GEO
Project description: Not available
| S-EPMC6686910 | biostudies-literature
Project description: Not available
| S-EPMC5601431 | biostudies-literature
Project description:The responses of the transcriptome of Synechocystis PCC 6803 to UV-irradiation were measured at time points over 36 h. Irradiation was provided by Sylvania soft white DuluzR compact fluorescent 23W bulbs (Osram Sylvania Ltd, Mississauga, Canada), a 20W RS UV-B medical light with a spectral maximum at 310 nm (model ‘TL’, Philips, Holland), and 15W black lights each with a spectral maximum at 368 nm (model F15T8-BL, General Electric, USA). Total quantum scalar irradiance was measured with a model QSL-100 meter (Biospherical Instruments Inc., San Diego, CA). The flux densities of the UV-A and UV-B components of the spectrum were measured with DIX series UV-B and 365A sensors, respectively, with a Spectroline DRC-100X digital radiometer (Spectronics Corporation, Westbury, NY). In these experiments full illumination represented a continuous photon flux density in the visible range of 330 μmol photons m-2 s-1, with UV-A and UV-B maxima of 3.8 x 10^6 and 0.8 x 10^6 mW m-2, respectively. All values reported were the incident fluxes within culture vessels at the immediate surface of the cell suspensions. Aliquot cultures (in duplicate) were harvested after 0, 15 min, 1 h, 3 h, 6 h, 12 h, 24 h and 36 h of UV-irradiation. For each time point, total RNA were isolated from stressed and unstressed cells, reverse-transcribed, differentially labelled (dye swapped), hybridized together (stressed versus unstressed samples) and analyzed with DNA glass microarrays (two slides per each time point) (Custom-commercial array : CyanoCHIP version 2.0, TAKARA). To identify differentially expressed genes, the median of the normalized ratio of Cy5/Cy3 intensity was calculated for each spot of the replicated dye-swap. The results of the analysis were carefully examined to exclude the dye effect between the 2 Cy-swapped arrays. Keywords: UV-irradiation, desiccation, Synechocystis PCC 6803, cyanobacteria, time course, transcription
2006-09-04 | GSE4606 | GEO
Project description:Time-resolved heat stress response of Saccharomyces cerevisiae
| PRJNA134643 | ENA
Project description:We have adapted the eXcision Repair-sequencing (XR-seq) method to generate single-nucleotide resolution dynamic repair maps of UV-induced cyclobutane pyrimidine dimers (CPDs) and (6-4) pyrimidine-pyrimidone photoproducts [(6-4)PPs] in the Saccharomyces cerevisiae genome. We find that these photoproducts are removed from the genome primarily by incisions 13-18 nucleotides 5’ and 6-7 nucleotides 3’ to the UV damage that generate 21-27 nt-long excision products. Analyses of the excision repair kinetics both in single genes and at the genome-wide level reveal strong transcription-coupled repair of the transcribed strand (TS) at early time points followed by predominantly non-transcribed strand (NTS) repair at later stages. We have also characterized the excision repair level as a function of transcription level. The availability of high-resolution and dynamic repair maps should aid in future repair and mutagenesis studies in this model organism.
2018-04-12 | GSE110621 | GEO
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
2020-09-04 | GSE136626 | GEO
Project description:MicroRNAs are central regulators of the T cell function. We explored RNA expression profiles over the initial 24 h of human CD4+ T cell activation. We found high similarity in time-resolved miRNA expression courses comparing independent activations and different donors. The detected miRNA expression patterns could be grouped into six classes only, each with a defined time course. MiR-155-5p known for its role in T cell immunity showed the most prevalent expression changes, quantified with an hourly increase of about 60 molecules/cell. As demonstrated for miRNA-155-5p, the analysis of time-resolved miRNA and mRNA expression data allowed to increase the validation rate of predicted miRNA targets to close to 90 %. Combining our time-resolved expression analysis with an absolute quantification of miRNA expression changes, gives new insights into miRNA regulatory networks and indicates the functional dominance of specific miRNAs within the early T cell activation.
2020-09-04 | GSE136625 | GEO
Project description:Method development for high-resolution spatially-resolved proteome mapping of tissue heterogeneity. Laser microdissection was coupled with nanodroplet sample preparation and ultrasensitive LC-MS.
2018-07-03 | PXD008844 | Pride