Project description:Genome editing was conducted on a t(3;8) K562 model to investigate the effects of deleting different modules or CTCF binding sites within the MYC super-enhancer. To check mutations after targeting with CRISPR-Cas9 we performed amplicon sequencing using the Illumina PCR-based custom amplicon sequencing method using the TruSeq Custom Amplicon index kit (Illumina). The first PCR was performed using Q5 polymerase (NEB), the second nested PCR with KAPA HiFi HotStart Ready mix (Roche). Samples were sequenced paired-end (2x 250bp) on a MiSeq (Illumina).
Project description:Chromatin immunoprecipitation analysis of CENH3 in the Arabidopsis thaliana accessions Col-0, Ler-0, Cvi-0 and Tanz-1 was performed in order to align reads to PacBio HiFi genome assemblies which contain complete centromere repeat arrays.
Project description:The Periconia genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia is widespread in many habitats but little is known about its ecology. Several species produce bioactive molecules, among them, Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. The strain CNCM I-4278, here identified as P. digitata was able to inhibit the plant pathogen Phytophthora parasitica. Since P. digitata has great potential as biocontrol agent and the only other genome available in the Periconiaceae family is that of Periconia macrospinosa, which is quite fragmentary, we generated long-read genomic data for P. digitata. Thanks to the PacBio Hifi sequencing technology, we obtained a high-quality genome with a total length of 38,967,494 bp, represented by 13 haploid chromosomes. The transcriptomic and proteomic data strengthen and support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will also contribute in our understanding of the Eukaryotic tree of life. Not least, opens new possibilities to the biotechnological use of the species.
Project description:The Periconia genus belongs to the phylum Ascomycota, order Pleosporales, family Periconiaceae. Periconia is widespread in many habitats but little is known about its ecology. Several species produce bioactive molecules, among them, Periconia digitata extracts were shown to be deadly active against the pine wilt nematode. The strain CNCM I-4278, here identified as P. digitata was able to inhibit the plant pathogen Phytophthora parasitica. Since P. digitata has great potential as biocontrol agent and the only other genome available in the Periconiaceae family is that of Periconia macrospinosa, which is quite fragmentary, we generated long-read genomic data for P. digitata. Thanks to the PacBio Hifi sequencing technology, we obtained a high-quality genome with a total length of 38,967,494 bp, represented by 13 haploid chromosomes. The transcriptomic and proteomic data strengthen and support the genome annotation. Besides representing a new reference genome within the Periconiaceae, this work will also contribute in our understanding of the Eukaryotic tree of life. Not least, opens new possibilities to the biotechnological use of the species.
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
