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RNA-seq analysis of lung-infiltrating neutrophils from WT and Atgl-cKO mice

ABSTRACT: RNA-seq analysis of lung-infiltrating neutrophils from WT and Atgl-cKO mice

PROVIDER: PRJEB38957 | ENA |

REPOSITORIES: ENA

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RNA-seq analysis of lung-infiltrating neutrophils from WT and Atgl-cKO mice

Project description:Atglflox/flox (B6N.129S-Pnpla2tm1Eek/J), S100A8-cre+/- (B6.Cg-Tg(S100A8-cre,-EGFP)1Ilw/J) mice were obtained from The Jackson Laboratory. Atglflox/flox mice were bred to S100A8-cre+/- mice to generate Atglflox/WTS100A8-cre+/- mice, which were backcrossed onto Atglflox/flox mice to generate Atglflox/floxS100A8-cre+/- mice (Atgl neutrophils-specific knock out, Atgl-cKO). Age-matched littermate Atglflox/flox mice were used as wild-type (WT) controls. To compare of the gene expression of the lung-infiltrating neutrophils isolated from Atgl-cKO mice and their WT littermates, AT3-g-csf cells were injected into the fourth mammary fat pads of female WT and Atgl-cKO mice (10-week-old, n = 4/group). The AT3-g-csf cell line is based on a murine breast cancer cell line (AT3) derived from MMTV-PyMT tumors in the C57BL/6 background, and further constructed to overexpress granulocyte-colony stimulating factor (G-CSF) for induction of the host inflammatory condition. At day 10 (pre-metastatic stage), the mice were euthanized and then Ly6G+ neutrophils were isolated from lung by using anti-Ly6G MicroBead Kit (Miltenyi Biotec) following manufacturer’s instructions. The isolated neutrophils were analyzed by flow cytometry and the cells with a > 95% purity were used for the next procedure. Total RNA was isolated from neutrophils using the miRNeasy Mini kit (Qiagen) and the transcriptional profiles of neutrophils were analyzed by RNA sequencing.

2020-06-28 | E-MTAB-9235 | biostudies-arrayexpress

RNA sequencing of blood and lung neutrophils from tumor-bearing mice

Project description:To investigate the difference among neutrophils circulating in the blood, and those infiltrating in the metastatic organ, we isolated peripheral blood (PB) and lung neutrophils from AT3 tumor-bearing mice. Total RNA was isolated from neutrophils and the transcriptional profiles of neutrophils were analyzed by RNA seq.

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RNA-seq of lung myeloid cells from WT and Ptgs2-cKO mice

Project description:To investigate the role of the COX-2-dependent lung fibroblast program in reprogramming lung myeloid cells, we generated fibroblast-targeted Ptgs2 conditional knockout mice by crossing Pdgfra-Cre mice with Ptgs2flox/flox mice. Then we isolated two primary types of lung resident DCs-CD103+ conventional DC (cDC1) and CD11b+ conventional DC (cDC2), and lung monocytes from WT and Ptgs2 cKO mice by fluorescence-activated cell sorting and performed RNA sequencing.

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Single-cell transcriptional profiles of lung CD45+ immune cells from WT and Ptgs2-cKO mice

Project description:To better understand the role of the COX-2-dependent lung fibroblast program in modulating the lung immune microenvironment, we generated fibroblast-targeted Ptgs2 conditional knockout (cKO) mice by crossing Pdgfra-Cre mice with Ptgs2flox/flox mice. Then we determined how Ptgs2 deficiency in CD140a+ fibroblasts alters the lung immune microenvironment by performing single-cell RNA sequencing on lung CD45+ immune cells from WT and Ptgs2-cKO mice.

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RNA sequencing of neutrophils residing in bone marrow, peripheral blood and lung

Project description:Generation of organ-infiltrating neutrophils occurs in hematopoietic tissues and organs, such as bone marrow and spleen, in response to tumor- and host-derived factors. The de novo expanded neutrophils then egress from hematopoietic sites, circulate through the blood vessels and infiltrate into the organ interstitia and parenchyma. During above trafficking process, neutrophils can undergo phenotypic and functional changes in response to tissue environments. To determine the difference among neutrophils residing in the hematopoietic site—BM, circulating in the blood, and those infiltrating in the metastatic organ, the transcriptional profiles of neutrophils were analyzed by RNA sequencing. 4T1 cells were injected into the fourth mammary fat pads of female syngeneic BALB/cJ mice (8-week-old, n = 3). At day 10 (pre-metastatic stage), the mice were euthanized and then CD45+CD11b+Ly6G<high>Ly6C<med> neutrophils from bone marrow (BM), peripheral blood (PB) and lung were isolated by fluorescence-activated cell sorting. Total RNA was isolated from neutrophils using the miRNeasy Mini kit (Qiagen) and the transcriptional profiles of neutrophils were analyzed by RNA sequencing

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The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae pneumonia in wild type (WT) mice [mRNA]

Project description:These studies profiled the expression of mRNAs and microRNAs (miRs) in lung neutrophils in WT mice during S. pneumoniae pneumonia and performed in depth in silico analyses. Lung neutrophils were isolated 24 hours after intratracheal instillation of PBS or S. pneumoniae, and mRNAs and miRs differentially expressed (DE) between S. pneumoniae- and PBS-treated samples were identified using microarrays.

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The mRNA and microRNA (miR) transcriptome of lung neutrophils during S. pneumoniae (SP) pneumonia in wild type (WT) mice [miRNA]

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RNA-seq of lung myeloid cells from WT and Ptgs2-cKO mice

Project description:RNA-seq of lung myeloid cells from WT and Ptgs2-cKO mice

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Next Generation Sequencing Facilitates Quantitative Analysis and Comparisions of Bone Marrow, Blood and Tumor-infiltrating Neutrophils

Project description:We report that tumor-infiltrating neutrophils are significantly different from their bone marrow and circulating neutrophils counterparts. We generated a heatmap clustering of the differentially expressed genes between the neutrophils from the three compartments, and identified four distinct gene clusters. Notably, genes in cluster 1 were down-regulated in tumor neutrophils, and comprised of genes involved in the adaptive immune response (GO:0002250). By contrast, genes in cluster 4 were up-regulated in tumor neutrophils, and consisted of genes involved in chemokine-mediated signalling pathway (GO:0070098) and positive regulation of cellular metabolic process (GO:0031325). We observed several cellular metabolic processes were up-regulated, suggesting a change in the metabolic signature of neutrophils that infiltrate the tumor. In conclusion, the distinct metabolic signature led us to hypothesize that the pronounced glycolytic profile of tumor-infiltrating neutrophils mediates pro-tumoral activity and PDAC progression.

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