10X genomics single cell RNA sequencing of tumor sections from tumor bearing KrasG12D/+Lkb1fl/fl(KL) mice after Ad-cre injection for 10 weeks
Ontology highlight
ABSTRACT: 10X genomics single cell RNA sequencing of tumor sections from tumor bearing KrasG12D/+Lkb1fl/fl(KL) mice after Ad-cre injection for 10 weeks
Project description:LKB1 deficiency is widely acknowledged to induce immune-desert tumors in the non small cell lung cancer. Dissecting the "cold" tumor microenvironment (TME) would promote a better understanding of mechnism of the immune evasion triggered by LKB1 loss, thereby facilitating to seek therapeutic targets. Here, we exploited single-cell RNA sequencing to show the immune landscape of genetically engineered mouse model (GEMM) bearing a conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) with or without Lkb1 conditional knockout (Lkb1fl/fl). The heterogeneity of TME and celler communication were analyzed.
Project description:Tumor-infiltrating cells comprise many celltypes, including monocytes, macrophages, dendritic cells, neutrophils, stromal cells and epithelial cells, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map cell heterogeneity in non-small cell lung cancer mouse model. We uncovered 11 cell types in tumor sections, most of which were reproducibly found across tumor bearing mice. we obtained a series of genes which expression levels were very low, such as cytokines and chemokines. It is very helpful for us to understand the signal cascade and ligands-receptors interaction between different cell types.
Project description:Comparative gene expression profiling analysis of RNA-seq data in CD45- lung tumor cells from tumor-burdened lungs of KrasLSL-G12D/+Lkb1fl/fl and KrasLSL-G12D/+Lkb1fl/flUsp25-/- mice 10 weeks after they were intranasally injected with Ad-Cre.
Project description:mRNA transcriptome sequencing of tumor cells, TRMs, MDMs, Monocytes and CD8+ T cells from tumor lungs of KrasLSL-G12D/+Lkb1fl/fl (KL), KrasLSL-G12D/+Lkb1fl/flGpx4m/m(KLG4) after Ad-cre injection and tamoxifen treatment
Project description:Ribosome profiling on sections taken from a kidney tumor For two tumors: 2 sections of normal tissue and 4 samples of tumor tissue, for another two tumors 1 section of normal tissue and 1 section of tumor tissue
Project description:5000 target cells per sample where sequenced from 2 gastric tumor samples and 1 sample of adjacent gastric mucosa Twist2Cre;Lkb1fl/+;RosaRTdtomato+/- mice. Drop-seq 10X Genomics (10X v3 library kit) was used for single cell barcoding and library preparation. Samples were sequenced with Novaseq6000.