Project description:Bulk RNA-sequencing experiments were performed to analyze the transcriptomic effects of such integrations into two newly established genomic safe harbor sites. Jurkat and HEK293T cells were edited to integrate CMV-mRuby expressing cassette into Rogi2 genomic safe harbor site using Cas9 RNP
Project description:BY4741（Δyrr1）exhibited better vanillin tolerance to vanillin than that of wildtype strain. To assess transcriptional differences between these two strains. Yrr1p is a transcriptional factors which activated genes related to multidrug resistance.The transcriptome of BY4741 and BY4741（Δyrr1）under vanillin stress or vanillin free conditions were conducted,respectively
Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)
Project description:The modification of Ser 5 is important for the relocalization of RNAP II upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. The 5A strain carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with alanine followed by 7 wild-type-sequenced repeats.
Project description:Genomic safe harbors (GSHs) are utilized as an ideal integration site for generating transgenic organisms and cells. Discovery of GSHs is one of the crucial factors for the advancement of basic and applied biology in the species. Such GSHs were discovered in Pv11 (Polypedilum vanderplanki) cell line, which can survive extreme desiccation. To identify the integration sites, high-molecular-weight genomic DNAs were extracted. The DNA libraries were prepared and sequenced with a Nanopore MinION sequencer. In the way to confirm that GSHs loci are localized in open chromatin regions we prepared ATAC-seq libraries, which were sequenced in Illumina HiSeq2500.
Project description:In this study we have deleted four metabolic genes (HIS3, LEU2, URA3 and MET15) in their sixteen possible combinations. These strains are following: knockout of HIS3, LEU2, URA3, MET15; knockout of HIS3, LEU2, MET15; knockout of HIS3, URA3, MET15; knockout of LEU2, URA3, MET15; knockout of HIS3, LEU2, URA3; knockout of HIS3, MET15; knockout of LEU2, MET15; knockout of URA3, MET15; knockout of HIS3, LEU2; knockout of HIS3, URA3; knockout of LEU2, URA3; knockout of MET15, knockout of HIS3; knockout of LEU2; knockout of URA3 and prototrophic strain. We grew the 16 strains in synthetic complete media (SC), and sampled for transcriptomincs in triplicates at mid-exponential phase (OD value of 0.8).
Project description:Transctriptome profiling of CTD-14 repeats, 2A, 5A mutants responding to 0.7N NaCl for 30mins. The study shows that phosphorylation at Ser5 sites plays a role in normal induction and repression of genes upon NaCl stress. The CTD14 strains harbors a plasmid expressing RPB1 with 14 wild-type CTD repeats. 5A strains carries a plasmid expressing a chimeric RPB1 in which the CTD was composed of 5 repeats of CTD-serine 5 substituted with Ala followed by 7 wild-type-sequenced repeats. The 2A strains carrys 8 repeats of CTD-serine 2 substituted with alanine followed by 7 wild-type-sequenced repeats.
