Project description:We have examined the changes that occur in microRNA (miRNA) expression levels in peripheral blood mononuclear cells (PBMC) collected from paired pre- vs. post-tumor removal samples in order to characterize the way lung tumor removal affects gene expression in peripheral immune cells. 5 miRNAs were expressed at significantly higher levels before vs. after tumor removal. Significant number of genes that were identified computationally as targets of the miRNAs and negatively correlated with the miRNA expression were transcription factors.
Project description:We have examined the changes that occur in microRNA (miRNA) expression levels in peripheral blood mononuclear cells (PBMC) collected from paired pre- vs. post-tumor removal samples in order to characterize the way lung tumor removal affects gene expression in peripheral immune cells. 5 miRNAs were expressed at significantly higher levels before vs. after tumor removal. Significant number of genes that were identified computationally as targets of the miRNAs and negatively correlated with the miRNA expression were transcription factors. miRNA expression changes were compared between 11 pre and post surgery NSCLC lung cancer samples.
Project description:MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post-transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack ability to identify novel miRNAs and accurately determine expression at a range of concentration. Deep or massively parallel sequencing methods are providing suitable platforms for genome wide transcriptome analysis and have the ability to identify novel transcripts. The results of analysis of small RNA sequences obtained by Solexa technology of normal peripheral blood mononuclear cells, tumor cell lines K562 (chronic myelogenous leukemia) and HL60 (acute promyelogenous leukemia) are presented. Custom computation pipelines were used to generate expression profiles of known and for identification of novel miRNAs. Some of the highly expressed miRNAs in the leukocytes include several members of the let 7 family, mir-21, 103, 185, 191 and 320a. Comparison of the miRNA profiles of normal versus K562 cells or HL60 revealed a specific set of differentially expressed molecules. Correlation of the miRNA with that of mRNA expression profiles, obtained by microarray, revealed a set of target genes showing inverse correlation with miRNA levels. Our computational pipeline also predicted a number of novel miRNAs. Some of the predictions were validated by realtime RT-PCR and or RNAase protection assay. The small RNA population from four samples - Two Normal Peripheral blood mononuclear cells (PBMC) samples, K562 cell line (This cell line is used as a model to study Chronic Myelogenous Leukemia), HL60 (This cell line is used to study acute promyelogenous leukemia) was sequenced using Solexa technology.
Project description:We found that peripheral blood mononuclear cells (PBMCs) (from subjects with allergy to nickel) stimulated with nickel were characterized by a specific miRNA signature that were different from vehicle-stimulated PBMCs.
Project description:Purpose: To infer interactions between circulating breast cancer cells and peripheral mononuclear cells using bioinformatics analysis of single cell RNA-sequencing. Methods: Filter based method for capturing single cells from 7.5mL of blood from patients with breast cancer, followed by single cell RNA-sequencing. Results: Transcriptomes predicted for two CTC populations with distinct expression profiles and interactions with peripheral blood mononuclear cells.
Project description:This SuperSeries is composed of the following subset Series: GSE33837: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) [miRNA] GSE33877: Comparative Expression Profile of miRNA and mRNA in Primary Peripheral Blood Mononuclear Cells Infected with Human Immunodeficiency Virus (HIV-1) [mRNA] Refer to individual Series
Project description:This SuperSeries is composed of the following subset Series: GSE33387: NanoString miRNA profiling of peripheral blood mononuclear cells from HIV-1-infected elite suppressors, viremic patients, and uninfected control donors GSE33492: TaqMan Peripheral blood mononuclear cell miRNA profiles of HIV-1-infected elite suppressors, viremic patients, and uninfected control donors Refer to individual Series
Project description:This study aimed to identify transcription networks and signatures of bovine peripheral blood mononuclear cells in response to LPS stimulation. A total of 464 genes including at least 17 transcription factors were identified to be significantly induced by LPS using a high density bovine oligonucleotide microarray. The network analysis revealed that alternation in gene expression was regulated by transcription factors through potential interaction within the pathway networks in the LPS stimulated cells. Our results demonstrated that specific pathway networks are responsible for transcription regulation in bovine peripheral blood mononuclear cells in response to pathogen components such as LPS. One class unpaired: Bovine Peripheral Blood Mononuclear Cells from 10 BLV positive cattle are divided into 2 groups: 5 treated with PBS in vitro for 2h serve as controls. The remaining 5 samples are stimulated with LPS in vitro for 2h.