Sentences with phrase «with gene expression analysis»

Feline: Defining Relevant Pathways in Feline Injection - Site Sarcomas with Gene Expression Analysis D08FE - 001, Marlene L. Hauck, Grant Amount: $ 82,123

In the lab, the scientific team used an approach that combined functional RNAi analysis with gene expression analysis in breast cancer - derived cell lines and in human breast cancers replicated in mice.

Not exact matches

In subsequent analyses, striking losses in gene expression were observed in genomic regions that had become increasingly methylated with age, whereas regions that had become less methylated showed increases in gene expression.

First, they did a quantitative analysis of the anatomy of related fossils and extant animals to generate a hypothesis about the transition; next, they searched for possible shifts in gene expression that correlated with the transition.

The tool acts with surgical precision to replace only abundances that have most likely dropped out and can be used in any type of single - cell gene - expression analysis.

Functional analyses indicate that MFSD12 encodes a lysosomal protein that affects melanogenesis in zebrafish and mice, and that mutations in melanocyte - specific regulatory regions near DDB1 / TMEM138 correlate with expression of ultraviolet response genes under selection in Eurasians.

Single - cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4 - CTLs, compared with CD4 + T cells in the central memory (TCM) and effector memory (TEM) subsets.

Evan Paull, a graduate student in Stuart's lab at UC Santa Cruz (now at Columbia University), led the computational analyses, which involved integrating the phosphoproteomic data with genomic and gene expression datasets to provide a unified view of the activated signaling pathways in late stage prostate cancer.

Separate analyses in which relative expression values were normalized with the relative expression values of each control gene yielded similar results.

(B, C) Flow cytometric analysis of HIV - 1 gene expression in (B) mock infected or (C) latently infected CD4 + T cells under non-polarizing conditions, either at the basal state or after reactivation with antibodies against CD3 and CD28.

The authors next took 997 tumors in the discovery set, integrated copy number and gene expression data, and performed clustering analyses to identify subgroups of tumors with distinct features and clinical outcomes.

Analyses were performed with 5 animals per group (control, 3 h of hypoxia, and 24 h or recovery after 3 h hypoxia) to decrease bias that may be introduced by donor - specific gene expression patterns.

Furthermore, we have validated and extended the conclusions of our model system with a detailed analysis of Î ± 2 integrin gene expression and its significance in human breast and prostate cancer.

This will be achieved by exposing the coral to seawater with high calcium concentrations to induce an alteration in gene expression profiles, identified using a DNA microarray analysis.

The Stylophora pistillata gene expression profile was analyzed with Partek Genomics Suite ™ software (Fig. 3A) in a principal component analysis (PCA).

The principal component analysis revealed that aging explains ~ 16 % of protein expression variability and is associated with Gene Ontology terms transmembrane, integral / intrinsic membrane, endoplasmic reticulum and mitochondrion.

Deeper analyses, revealed that the RNA expression pattern of a rare variant of the NCAN gene was highly correlated with that of the previously suggested susceptibility genes for developmental dyslexia.

Along with the cellular genes emphasized from the microarray analysis, two genes that are suspected to be involved in the scleractinian coral calcification process were tested for expression (Figs. 5A and 5B).

Significant gene sets with differential expression in adipose tissue of diabetic compared with nondiabetic co-twins (GSEA analysis with q < 0.05)

In line with previous studies12, 13,15,17,20 our analyses show that the investigation of the impact of post-mortem ischemia in tissue transcriptomes is essential to properly interpret gene expression estimates obtained from post-mortem tissue samples.

The researchers found 77 women with matched imaging and gene expression data, so they combined their analyses of visceral fat and glycolysis.

Nick Owens, a post doc in Mike Gilchrist's lab, who developed the computational analysis, said: «This study improves our ability to understand the way gene expression changes with time, and from this we gain insight into the logic of how gene expression is regulated.

Proteomic analysis to profile protein abundance resulted in the identification and relative quantification for 912 proteins with two or more unique peptides and 86 proteins with significant abundance changes after treatment with the neurotoxins, while microarray analyses to profile gene expression revealed 181 genes with significant changes in mRNA after treatment.

Further comparative genomic and transcriptomic analyses showed infection severity correlated with the expression levels of certain genes shared by nearly all E. coli, including genes involved in motility and nutrient utilization.

Analysis of the genes expressed by tumors treated with MIA - 602 indicates that it suppresses the expression of tumoral inflammatory cytokines.

Also, gene expression analysis showed that ERBB2 expression correlates with outcome (higher expression = poor prognosis).

For the analysis of gene expression in blastocysts, total RNA was isolated and purified from three pools of 10 blastocysts produced in vivo or in vitro (KSOM supplemented with 10 % FCS or in the presence of 1 g / L BSA) using the RNeasy Micro Kit (Qiagen)[18].

Treated and untreated NSCs and neurons were then interrogated with global gene expression analysis to explore the mechanisms of action of amiodarone HCl.

The Wasserman laboratory focuses on the creation, evaluation and application of computational methods for the analysis of genome sequences, with international strength in the study of cis - regulatory elements regulating gene expression.

Their gene expression analysis throughout the protocol matched that of a previously published profile for hESCs [24], which included the significant upregulation of mesodermal and chondrogenic markers (PDGFRB, SOX6, SOX9, ACAN, COL2A1 types A and B), with the more mature COL2A1 type B splice variant [42] being more highly expressed by the end of stage 3.

Correlation of differentially expressed transcripts was detected by hierarchical clustering of expression values with the Cluster version 2.11 software [52] applying mean centering and normalization of genes and arrays before the computational clustering analysis.

RNAseq analysis of liver, muscle and adipose tissue confirmed that Lyplal1 expression was ablated with minimal additional changes in gene expression.

To investigate the underlying mechanisms, we undertook (1) bioinformatic, functional genomic annotation and human osteoblast expression studies; (2) gene - function prediction; (3) skeletal phenotyping of 120 knockout mice with deletions of genes adjacent to lead independent SNPs; and (4) analysis of gene expression in mouse osteoblasts, osteocytes and osteoclasts.

Unbiased clustering analysis of P (+) neurons revealed four different classes, each with distinct cell surface receptor gene expression profiles.

Indeed, 30 % of all transcripts identified by cap - analysis of gene expression (CAGE) tags derived from human embryonic tissues have been associated with repetitive elements, and 16 % are retrotransposons [14].

Intestinal permeability was assessed by Ussing chamber; epithelial cell (EC) ultra-structure by electron microscopy; RNA expression of genes coding for junctional proteins by Q - real - time PCR; immune response by in - vitro antigen - specific T - cell proliferation and cytokine analysis by cytometric bead array; intestinal microbiota by fluorescence in situ hybridization and analysis of systemic antibodies against intestinal microbiota by surface staining of live bacteria with serum followed by FACS analysis.

Grant 1557: High - Resolution Cytogenetic Analysis of Histiocytic Malignancies and Development of a Targeted Assay to Screen for Expression Level Changes Dr. Matthew Breen, PhD Project Goal: The goal of this project is to narrow down the search for genes playing a key role in Histiocytic Malignancies and thus move a step closer to developing targeted therapies for canine patients diagnosed with this devastating cancer.

Provided data analysis that included statistics package development with staff statisticians, and high throughput assay advent and development (immediate early gene expression); Taq - man primer - probe research and design using primer express.