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RNA-Seq analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

ABSTRACT: RNA-Seq analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

PROVIDER: PRJNA817820 | ENA |

REPOSITORIES: ENA

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RNA-Seq analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice

Project description:Purpose: The goals of this study are to compare CD115- monocytes to CD115+ monocytes from naïve and tumor-bearing mice (EL4) with high-throughput data analysis. Methods: CD115- monocytes and CD115+ monocytes were sorted by flow cytomentry separatly. Total RNA was extracted from cells using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and residual DNA was removed with a DNA-free Kit (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer’s instructions. Samples were loaded onto a 1% agarose gel before electrophoresis. DNA-free conditions were confirmed by SYBR Gold staining (Invitrogen). The quantity and the quality of RNA was evaluated by Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) and bioanalyzer (Agilent 2100; Agilent Technologies, Santa Clara, CA, USA). RNA-Seq libraries were prepared with 1 μg of total RNA from two biological replicates of each group using TruSeq Stranded mRNA LT Sample Prep Kit and analyzed by Illumina Sequencer (both from Illumina, San Diego, CA, USA). Results: We found 1,723 differetially expressed genes (DEGs) between CD115- monocytes and CD115+ monocytes (cutoff value was set at 2-fold). DEGs of interest are invoved in granulocyte, transcription factors, mononuclear phagocytes, and angiogenesis. Conclusions: Our study represents the first detailed DEGs analysis of CD115- monocytes and CD115+ monocytes from naïve and tumor-bearing mice. Our results show that CD115- monocytes may have a closer relationship with neutrophils or PMN-MDSCs than the CD115+ monocytes. Also, our overall transcriptomic analysis further suggests that CD115- M-MDSCs and monocytes are separate subsets of monocytic cells.

2022-03-22 | GSE199008 | GEO

Baseline CD11b+ CD115+ Co-housed vs specific pathogen free monocytes

Project description:The immune system of SPF mice is dominated by naïve phenotype immune cells, especially within the T cell compartment, and resembles that of neonatal humans (Beura et al., 2016; Reese et al., 2016). Sequential infection of SPF-housed laboratory mice with common experimental pathogens, such as MHV, MCMV, Listeria monocytogenes, LCMV, and influenza A virus (Berton et al., 2022; Reese et al., 2016), or cohousing (CoH) SPF mice with pet store mice carrying multiple pathogenic and commensal bacteria, viruses, and/or fungi (Beura et al., 2016) induces immune system alterations and maturations that more closely resemble the adult human immune system. Such microbial exposure drastically alters the composition and function of the immune system of laboratory mice, which can significantly influence the overall outcome (and survival) to subsequent infection. Here we report CD11b+ CD115+ monocytes sorted from female specific pathogen-free (SPF) C57BL/6N (B6) mice co-housed with petstore mice for 60 days are transcriptionally different than SPF CD11b+ CD115+ monocytes

2023-10-26 | GSE237883 | GEO

Single-cell transcriptional profiles of BM, PB and lung neutrophils from naïve (C57BL/6J), AT3, and AT3-gcsf tumor-bearing mice

Project description:To determine the effect of tumor-bearing vs. host neutrophilic inflammation on reinforcement of lung neutrophil-specific immunosuppressive function, we performed single-cell RNA sequencing (scRNA-seq) on BM, PB and lung neutrophils isolated from naïve (C57BL/6J), AT3, and AT3-gcsf tumor-bearing mice.

2022-12-12 | GSE217595 | GEO

Single-cell transcriptional profiles of BM, PB and lung neutrophils from naïve (BALBc/J) and 4T1 tumor-bearing mice

Project description:To better understand how lung neutrophils transcriptionally differ from other tissue neutrophils, we performed single-cell RNA sequencing (scRNA-seq) on BM, PB and lung neutrophils isolated from naïve (BALBc/J) and 4T1 tumor-bearing mice.

2022-12-12 | GSE217143 | GEO

Single-cell transcriptional profiles of different tissue-derived myeloid cells from naïve and MDA-MB-231 tumor-bearing humanized mice

Project description:To better understand how lung neutrophils transcriptionally differ from other tissue neutrophils, we performed single-cell RNA sequencing (scRNA-seq) on different tissue-derived myeloid cells isolated from naïve and MDA-MB-231 tumor-bearing humanized mice.

2022-12-12 | GSE217499 | GEO

RNA Sequencing of CD169+ lymph node macrophages isolated from naïve or tumor-bearing mice

Project description:CD169+ macrophages residing in naïve or tumor-draining inguinal lymph nodes revealed their protective role in tumor metastasis

2021-06-02 | E-MTAB-8482 | biostudies-arrayexpress

scRNA-seq of lung CD140a+ mesenchymal cells from naïve or tumor-bearing CD140aEGFP reporter mice

Project description:To investigate the CD140a+ mesenchymal cell heterogeneity in the lung in both steady and tumor-bearing conditions, we utilized CD140aEGFP reporter mice, and purified CD140a+ lung mesenchymal cells from naive and tumor-bearing mice and performed scRNA-seq.

2022-11-01 | E-MTAB-11902 | biostudies-arrayexpress

Whole transcriptome analysis of Lingual Sensory Neurons in Naïve and Tongue-Tumor Bearing Male and Female Mice

Project description:Using RNA sequencing of FACS sorted retro-labeled sensory neurons innervating tongue tissue, we determined changes in transcriptomic profiles in males and female mice under naïve as well as tongue-tumor bearing conditions Our data revealed the following interesting findings: 1) Naïve female neurons innervating the tongue exclusively expressed immune cell markers such as Csf1R, C1qa and others, that weren’t expressed in males. 2) Male neurons were more tightly regulated than female neurons upon tumor growth; 3) While very few differentially expressed genes (DEGs) overlapped between males and females post-tumor growth, several biological processes (BPs) were similar between two sexes. However, additional distinct processes were sex-specific; 4) Post-tumor growth, male DEGs contained an equal mix of transcription factors, ligands, growth factors, receptors and channels, whereas female DEGs predominantly contained channels/receptors, enzymes, cytokines and chemokines.

2023-08-15 | GSE220448 | GEO

RNA Sequencing of CD169+ lymph node macrophages isolated from naïve or tumor-bearing mice

Project description:RNA Sequencing of CD169+ lymph node macrophages isolated from naïve or tumor-bearing mice

| PRJEB35312 | ENA

Expression data of Naïve Treg and Tumor associated Treg cells

Project description:Naïve Treg cells were purified from the resting spleens of FoxP3-GFP knock-in mice made in the 129/SvJ strain. Ascites Treg cells were tumor-associated FoxP3-GFP+ cells sorted from the tumor ascites of 129/SvJ mice IP-injected with 1 x 10e6 RMAS cells 5 days earlier; Spleen-T Treg cells were purified from the spleens of the same tumor-bearing mice. Keywords: in vivo samples Affymetrix MOE430v2 arrays were used to perform gene expression studies. The purity of the sorted Treg cells is >99%.

2008-10-31 | E-GEOD-13409 | biostudies-arrayexpress

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