Project description:Single cell RNA sequencing was performed on CD45+Ly6G-CD64+MerTK+ macrophages isolated from the lungs of mice 5 weeks after transplantation of 4T1-Luc mammary gland tumors. The purpose of this study was to determine the unique macrophage subsets present in the lungs of mice bearing mammary tumor metastases.
Project description:Primary objectives: Characterization of the macrophage population subset that is modulated by enteric neurons
Primary endpoints: Characterization of the macrophage population subset that is modulated by enteric neurons via RNA sequencing
Project description:The goal of this study was to identify mechanism of suppression of cDC1 in a model of genetically driven lung adenocarcinoma (KP). As part of the study we analyzed the transcriptional differences between cDC1 cell-sorted from healthy lung and those cell-sorted from KP bearing lungs.
Project description:mRNA transcriptome sequencing of tumor bearing lungs from KrasLSL-G12D/+Lkb1fl/fl, KrasLSL-G12D/+Lkb1fl/flIl1f9-/-(KL9) and KrasLSL-G12D/+Lkb1fl/flIl1f5-/-(KL5) or KrasLSL-G12D/+Tp53fl/fl, KrasLSL-G12D/+Tp53fl/flIl1f9-/-(KP9) and KrasLSL-G12D/+Tp53fl/flIl1f5-/-(KP5) after 10 weeks Ad-cre injection Tumor-burdened lungs from KL/KL5/KL9 mice and KP/KP5/KP9 mice were perfused through alveolar lavage and cardiac lavage with PBS, dry it quickly, and then homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis. Poly(A) mRNA was subsequently purified from 10μg total RNA using NEBNext Oligo d(T)25 Magnetic Beads Isolation Module. First-strand complementary DNA was synthesized with NEBNext RNA First-Strand Synthesis Module. NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module was used for the synthesis of the complementary strand of first-strand cDNA. The resulting double-stranded DNA was purified and Vazyme TruePrep DNA Library Prep kit V2 was used to prepare libraries followed by sequencing on an Illumina Hiseq X Ten platform with 150-bp paired-end reads strategy (Novogene). Quality control of mRNA-seq data was performed by using Fatsqc (v0.11.9) and low-quality bases were trimmed by Trim_galore (0.6.4_dev). All RNA-seq data were mapped to the mouse genome (Mus_musculus_Ensemble_94) by Hisat2 (v.2.0.5) and allowed a maximum of two mismatches per read. Gene expression level was calculated by FeatureCounts (v.2.0.0) with default parameters and normalized by FPKM (Fragments Per Kilobase of exon model per Million mapped fragments).
Project description:We studied the impact of DT treatment (Treg depletion) on NK cells (CD3-, NKp46+, DX5+) in axillary TDLNs and lungs of tumor bearing Foxp3GFP-DTR mice . Here we generated RNAseq data from sorted NK cells from DT or PBS treated Foxp3GFP-DTR mice bearing 100mm2 mammary tumors from lungs, axillary TDLNs