CM-CBX-aPD1
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB46159 | ENA |
REPOSITORIES: ENA
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Project description:Comparison of transcriptome data in tumors from mice treated with combinations of mitomycin C, oncolytic HSV-1, anti-PD-1 and anti-CTLA-4.
2022-03-01 | GSE195924 | GEO
Project description:Transcriptional profiling of Acinetobacter baumannii ATCC17978 cells comparing each treated 1/2MIC Cm, 1/2MIC HBA and combination of 1/4MIC Cm and HBA cells with same volume of ethanol treated. Based on the gene expression, we analyzed results to confirm the relation between Cm and HBA to antibacterial synergism against A. baumannii. (Concentrations treated respectivly in all samples were adjusted to add same volume of Cm, HBA and combination)
2015-03-24 | GSE67173 | GEO
Project description:Purpose: The goals of this study are to compare transcriptomic profiling (RNA-seq) of BMDMs activated by CM generated from CO-Fibs and PH-Fibs and to evaluate the mechanisms how healthy and pulmonary hypertensive adventitial microenvironment maintain or activate macrophage phenotypes. Methods: Mouse BMDMs were treated with media conditioned by CO-Fibs (CO-CM) or PH-Fibs (PH-CM) or left untreated (UNX). Each CM was pooled from 5 different fibroblast populations. Total RNA was purified using NucleoSpin RNA Isolation kit (Machery-Nagel, www.mn-net.com) according to the manufacturer’s instructions. RNA quantity and quality were evaluated using NanoDrop and Bioanalyzer. For Transcriptomics analysis, RNA-Seq library preparation and sequencing were conducted using a NuGen universal plus mRNA-Seq kit. Sequencing was performed on Illumina NovaSEQ6000 system, using the paired-read 2x150 cycle option. RNA-Seq reads were generated using Illumina NovaSEQ6000 analysis pipeline. The read quality of all the samples were checked using FastQC v0.11.5. Adapter trimming, quality control, and base correction were performed by AfterQC (Chen et al., 2017). The sequencing reads in the FASTQ files of all the samples were aligned to the Mus musculus reference genome (Mus_musculus. GRCm38v91) with Spliced Transcripts Alignment to a Reference (STAR) version 2.6.0c. We next applied featureCounts v1.6.2 to assign reads to genes using mouse transcript annotations as a guide. EdgeR in R was used for data normalization and differential expression analysis of RNA-Seq expression profiles with biological replication. The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR), and a cut-off criterion of FDR ≤ 0.05 was applied to identify differentially expressed genes. Individual gene expression was calculated as ‘reads per kilobase per million mapped reads’ (RPKM). Results: Using a standard data analysis workflow (STAR-featureounts-edgeR), our results showed that both CO-CM and PH-CM had significant, yet clearly different, effects on gene expression in BMDMs. Principal component analysis (PCA) of all 12,191 genes showed overall separation of CO-CM and PH-CM treated BMDMs from untreated BMDMs. To obtain insight into the underlying mechanisms through which microenvironments regulate macrophage phenotype and function in control and diseased conditions, we analyzed genes uniquely regulated by CO-CM or PH-CM vs. naïve BMDM using Ingenuity Pathway Analysis (IPA). Canonical signaling pathways identified by IPA demonstrated that CO-CM significantly inhibited inflammatory pathways (role of pattern recognition receptors), immune responses (PD-1, PD-L1 cancer immunotherapy pathway, Tec Kinase signal, and T cell exhaustion signal), lipid (3-phosphoinositide) metabolism and glycolysis suggesting a metabolically quiescent and anti-inflammatory phenotype. In contrast, when the microenvironment was dictated by disease (i.e., PH-CM), macrophages exhibited distinct upregulated canonical pathways, particularly those related to inflammation (iNOS, Toll-like receptor, NF-kB, TNFR, etc.) and activated immune responses (Th1 pathway, T cell exhaustion signaling pathway, dendritic cell maturation). Pathways involved in metabolism were also notably altered with increased NO and ROS production, and decreased oxidative phosphorylation indicating altered mitochondrial function. Conclusions: Results from our study provide the basis for a more systematic mechanistic understanding of the cross-talk between adventitial fibroblasts and macrophages in health and disease by revealing a comprehensive view of the macrophage transcriptomic and metabolomic landscape.
2021-03-16 | GSE165500 | GEO
Project description:Analysis of 3 subsets of primary human CD4+ T cells (naive, CM, EM) stimulated with anti-CD3, anti-CD28 and PD-L1/PD-L2 for 18 hours. we show that naive, EM, and CM T cell subsets had distinct gene expression profiles following PD-1 ligation.
2021-07-01 | GSE174860 | GEO
Project description:Human cardiomyocytes (CMs) differ from those of rodents in many aspects, and methods that effectively improve cardiac performance in rodents have been unsuccessful in humans, indicating a translational gap between humans and rodents in cardiac regeneration. The CM proliferation transition between the neonatal and adult stages is well-established in humans and rodents. The aim of the study is to analyze human atrial CM proliferation-transition for narrowing down the translational gap between humans and rodents in cardiac regeneration.At first we extracted decellularized samples (DS) from human atrial specimens collected during routine congenital cardiac surgery from children diagnosed with ventricular septal defect (VSD). The DS was next used for cell culture and proteomic analyses. The proteins (such as Agrin, BRP44, and insulin) identified in the proteomic analysis were further verified by testing their ability to promote CM proliferation. The results showed that the combination of agrin, BRP44, and insulin (ABI) enhanced the effect of agrin.To further confirmed the role of ABI on human CM proliferation, we performed RNA-seq on the ABI-treated HiPSC-CMs. The results showed that ABI induced abundant enrichment of cell-cycle associated genes, which highlighting the synergy of hormones and anti-oxidation/metabolism in human CM proliferation.
2024-08-16 | GSE240986 | GEO
Project description:Tumor mutation burden estimated with whole exome sequencing of 43 NSCLC patient tumors treated with anti-PD-1 + anti-CTLA-4
2018-02-15 | PRJEB24995 | EVA
Project description:Phaffomycetaceae sp. UFMG-CM-Y7052 isolate:UFMG-CM-Y7052 Genome sequencing
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