Project description:This aim of this experiment is to assess the genome-wide Rad2 occupancy in yeast Saccharomyces cerevisiae by ChIP-chip, in the absence of exogenous genotoxic stress. A related study involving ChIP-seq analysis of Rad2 occupany is also deposited at ArrayExpress under accession number E-MTAB-1595 ( www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1595 ).
Project description:In this study, we generate genomic maps of Mediator, Pol II, TBP, TFIIH, TFIIA, TFIIB, TFIIE, TFIIF, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type strains from Saccharomyces cerevisiae and in a mutant for the Mediator essential subunit Med10
Project description:In this study, we generate genomic maps of Mediator, Rad2, Pol II, TBP and TFIIH, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type strains from Saccharomyces cerevisiae. A related study involving ChIP-chip analysis of Rad2 occupany is also deposited at ArrayExpress under accession number E-MEXP-3875 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-3875 ).
Project description:In this study, we generate genomic maps of Mediator, Pol II, TBP and TFIIH, by ChIP coupled to next generation sequencing technology (ChIP-seq), in wild type (WT) strains and med17-ts mutants from Saccharomyces cerevisiae. Some of the data, concerning WT strains are also deposited at ArrayExpress under accession number E-MTAB-1595 (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1595). There are 2 series of experiment: 1- WT (see E-MTAB-1595) and mutants med17-98, med17-444, and med17-670 (this submission) 2- WT and mutant med17-444 (this submission).
Project description:We performed ChIP-seq analyses of Rad2, Mediator (Med17 and Med5) and RNA Polymerase II in Kin28-ts16 mutant, Med17-Q444P and Med17-Q444P/M442L mutants and in an Rpb9 deleted strain.
Project description:L. japonicus (Regel) Larsen cv, Gifu were initially obtained from Prof. Jens Stougaard<br>(University Aarhus, Denmark) and then self-propagated at the University of Seville.<br>Seeds were scarified and surface-sterilized,<br>germinated in 1% agar Petri dishes, and transferred to pots using a 1:1 (v/v) mixture<br>of vermiculite and sand as solid support.<br>Five seedlings were planted in each pot and grown<br>during 35 days in a growth chamber under 16/8 hours<br>day/night, 20/18M-oM-?M-=C, with a photosynthetic photon flux<br>density of 250 M-oM-?M-=mol/m2M-oM-?M-=s and a constant humidity of 70%.<br> Plants were watered with Hornum nutrient solution.<br>Drought was applied withholding irrigation for the reported period<br>of time and sample plants or leaves were harvested for further analysis.
Project description:Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed to profile the proteomes of Control and Palbociclib-treated HeLa cells. For protein identification and quantification, mass spectrometry data from fractionated samples (data-dependent acquisition, DDA; 6 fractions) and single-shot samples (data-independent acquisition, DIA) were utilized to construct a DDA library and a direct-DIA library, respectively. These libraries were computationally merged into a hybrid spectral library using Spectronaut software (Biognosys). Subsequent functional annotation was performed through Gene Ontology (GO) and InterPro (IPR) analyses using the InterProScan-5 tool against the non-redundant protein database. Additionally, protein family and pathway analyses were carried out using the Clusters of Orthologous Groups (COG) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.
Project description:Liquid Chromatography with tandem mass spectrometry (LC-MS/MS) identification of phosphorylation of control and Palbociclib-treated HeLa cells. For identification and quantification of protein, the single-shot subject samples (DIA MS data) were used to generate a direct-DIA library and computationally merged into a hybrid library in the Spectronaut software (Biognosys). For subsequent data analysis, Gene Ontology (GO) and InterPro (IPR) analysis were conducted using the InterProScan-5 program against the non-redundant protein database, and the databases COG (Clusters of Orthologous Groups) and KEGG (Kyoto Encyclopedia of Genes and Genomes) were used to analyze the protein family and pathway.
Project description:P388D1 murine macrophages were cultured in 85 mm tissue culture plates to about semi confluency. L. monocytogenes serotypes (1/2a EGD-e, 4a L99, 4b CLIP80459 and 4b F2365) were infected to the P388D1 cell monolayer at a MOI of 100 per eukaryotic cell. Infection was carried for 45 min and followed by addition of fresh medium containing 20 M-5g/ml gentamicin. The medium of the plates (containing 20 M-5g/ml gentamicin) infected with L. monocytogenes serotypes were replaced after 2 h post infection with fresh medium containing 50 M-5g/ml gentamicin. At each step the plates were washed extensively with 1x PBS. Incubation of the bacterial tissue culture plates was carried out in a humidified incubator for up to 4 h post infection.