Project description:Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to protocatechuic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.
Project description:Gene expression profiling of Blastobotrys raffinosifermentans LS3 cells based on 6.025 annotated chromosomal Blastobotrys raffinosifermentans LS3 sequences and 36 putative mitochondrial gene oligos was performed following exposure to gallic acid. Microarray data were successfully used to identify expression changes of main candidate genes involved in tannic acid degradation, protocatechuic acid degradation, β-oxidation, the glyoxylate cycle, the methyl citrate cycle and the catabolism of the branched-chain amino acids valine, leucine and isoleucine.
Project description:4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected inside IGS. Our data indicate that mostly rDNA units exhibit close proximity with pericentromeric regions in different chromosomes. We also detected the contacts within a rDNA unit and between rDNA units. Examination of rDNA genome-wide contacts in HEK 293T cells using 4C approach.
Project description:Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences. ************************ Data processing steps: FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000 Read density across the rDNA sequence was extracted using igvtools ************************
Project description:4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected inside IGS. Our data indicate that mostly rDNA units exhibit close proximity with pericentromeric regions in different chromosomes. We also detected the contacts within a rDNA unit and between rDNA units.
