Project description:Intent of the experiment: evaluate whether copy number gains and losses occur throughout the processing of passaging, i.e. test the genomic stability of the patient-derived xenograft models. DNA was extracted from frozen xenograft samples of different passages. KAPA DNA Library Preparation Kit was used to prepare DNA libraries, which were sequenced at low coverage on a HiSeq2000 (Illumina) with a V3 flowcell generating 50bp reads. Raw reads were aligned to the human reference genome version hg19 with Burrows-Wheeler Aligner software package and after duplicate removal further analyzed with QDNAseq to exclude known regions with low mapping quality, correct for the genomic wave and to count the reads per bin. Binned data were further segmented with the ASCAT (Allele-Specific Copy number Analysis of Tumours) algorithm.
Project description:Low-coverage whole genome of endometrium cancer derived organoids. Organoids were established from patients with endometrial diseases and DNA was extracted from low passage number and high passage number and compared with the primary tissue when available to investigate whether organoids retain the same genomic abnormalities and disease-associated features.
Project description:Whole-genome DNA libraries were prepared from a population of just under 100 Col/Ler F1 backcrossed to Col. Low-coverage whole-genome sequencing was used to map meiotic crossovers in this population following the protocol described in Rowan et al., 2015, doi: 10.1534/g3.114.016501.
