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.