Project description:We report the application of bulk RNAseq of live cells from pancreas of KPC or KPC-OG genetic mice at 6 weeks of age. These sponteneous tumors were unperturbed otherwise until timepoint.
Project description:Recently, Bailey et al (2016, Nature) defined four subtypes of pancreatic cancer that are associated with distinct histopathological characteristics and differential survival, namely, Squamous, Pancreatic Progenitor, Immunogenic, and ADEX (Aberrantly Differentiated Endocrine eXocrine). We set out to assess by RNASeq whether loss of CXCR2 was significantly associated with a specific PDAC subtype. Pancreatic tumors were harvested from KPC or KPC Cxcr2-/- mice at endpoint (n=5 v 5), RNA prepared, and RNASeq analysis carried out. Reads were analysed using the bcbio-nextgen framework (https://bcbio-nextgen.readthedocs.org/en/latest/). After quality control and adaptor trimming, reads were aligned to the mouse genome build (UCSC mouse mm10) using STAR. Counts for known genes were generated using the function featureCounts in the R/Bioconductor package \Rsubread\. The R/Bioconductor package edgeR was used to identify differentially expressed genes.
Project description:Experiment designed to study the effect of deregulated myc on pancreatic cancer progression and regression. In the KRasG12D/RosaMycER mouse model KRas and MycER are expressed exclusively in the pancreas, but MycER activity depends on Tamoxifen presence. For this experiment a mouse was treated with Tamoxifen during 3 weeks, the pancreas was collected and the epithelial cells were grown in vitro in the presence of 4-OHT (4-Hydroxytamoxifen, active form of Tamoxifen). RNAseq were preformed on the cell line treated as follows: 1- 4-OHT all the time. 2- EtOH 6h. 3- EtOH 12h. 4- EtOH 18h.
Project description:We report here that a EMMPRINs-specific cancer peptide vaccination, where the peptide was modified and synthesied as a multiple antigenic peptide (MAP), significantly inhibited tumor growth and metastases. Specifically, we describe changes in the gene expression profile as assessed by RNAseq in tumors derived from mice implanted with the colon tumorigenic carcinoma (CT26 cells), and vaccinated with either a control scrambled multiple antigenic peptide (Scr-MAP) or with an epitope-specific EMMPRIN multiple antigenic peptide (designated 161-MAP).
Project description:Bulk RNA sequencing of sorted peri-pancreatic LN cDC1s from different stages of neoplastic development in the KPC mouse model of pancreatic adenocarcinoma.