Project description:A subset of tumor-initiating cells (TIC) drives colorectal cancer (CRC) progression in serial mouse xenografts. The TIC compartment itself is heterogeneous and comprises hierarchically organized long-term TIC, tumor transient amplifying cells, and delayed contributing TIC. To address the genomic heterogeneity of the CRC TIC compartment, genome-wide high-coverage whole genome sequencing was performed on patient tumors (n=3), corresponding serially passaged TIC-enriched spheres, and serial xenografts.HIPO P002
Project description:The mouse renal cancer cell line RENCA was serially passaged in vivo using multiple implantation strategies (called Kidney, Tail and Lung) designed to replicate different aspects of primary tumour growth and metastasis. We have acquired methylomic data.
Project description:This DNA methylation dataset describes epigenomic changes in in vitro serially passaged primary and immortalized astrocytes, in the context of studies examining cellular aging patterns that are conserved in vivo and in vitro. Primary and fetal hTERT-immortalized astrocytes were grown under normoxic conditions and serially passaged. Longitudinal DNA samples were collected throughout passaging and DNA methylation was measured using the Infinium HumanMethylation850 BeadChip.
Project description:Tissue for normal colonic stem cell isolation was obtained via colectomy from a colorectal cancer patient. It was shown that the resected tissue and the in vitro-cultured organoids grown from tissue-derived adult stem cells do not harbor chromosomal alterations. For that purpose, genomic DNA from resected mucosa or genomic DNA from adult stem cell-derived organoids grown in a 3-dimensional culture system was compared to white blood cell genomic DNA obtained from the same individual. Furthermore, in vitro organoids which were cultured and serially passaged for several weeks did not acquire chromosomal alterations.
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
Project description:Analysis of anti-angiogenic therapy resistance in xenografts of patient glioma samples serially passaged across generations of athymic nude mice