Sentences with phrase «from microarray»

Differentially methylated regions from the microarray analysis with varying p values (between 0.0001 and 0.03 with FDR < 0.2) and fold differences (Log2 CPA / Controls between 1.1 and 0.5) at the probe level were selected for validation.

Signal: normalized log2 signal values from the microarray analysis.

The dotted black line represents the background intensity level from the microarray.

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).

The paper entitled, «How to get the most from microarray data: advice from reverse genomics,» was published online March 21, 2014 in BMC Genomics.

Apart from science and engineering, bioinformatics is a vital tool in microarray analysis due to the vast amounts of data that are generated from a microarray experiment.

(C — F) For a subset of genes (Table S1), the log10 normalized intensity values obtained from the microarrays (C — D) and from RNAseq in FPKM (E — F) are plotted against the log10 RQ values from TaqMan qRT - PCR assays.

Not exact matches

Natera uses a SNP microarray from Ilumina with a proprietary technology called Parental Support ™, which tests all 24 chromosomes and delivers results that are typically > 99 % accurate.

Larger biomarker signatures can be detected with technology from CDI Laboratories, which offers microarrays of functional human proteins (over 20,000 on a single array) to test the antibodies present in human liquid biopsy samples, such as blood, serum, plasma, CSF, or tissue lysates.

Microarrays are becoming a more commonly used tool in fields ranging from agriculture to zoology.

ONE OF THE FIRST THINGS MIKOVITS DID was to employ a microarray — a small tray seeded with DNA from nearly every known virus — to flag viral DNA in human white blood cells.

And he had some preliminary evidence: When he added DNA from malignant prostate tissue cells to a microarray, a novel retrovirus emerged.

The researchers analyzed microarray data of samples from German patients and from an IPF cohort of the Lung Tissue Research Consortium in the U.S.

Here we show that hybridization capture on microarrays can successfully recover more than a megabase of target regions from Neandertal DNA even in the presence of ~ 99.8 % microbial DNA.

To help identify genes and signaling pathways that may be influenced by zinc, Knoell and his team performed a genome - wide microarray analysis of lung tissue taken from zinc - deficient mice with sepsis.

Subjecting N. gonorrhoeae to the phenotypic microarray screening method for the first time, Sikora's team focused on seven proteins from the bacteria's cell envelope, which consists of the outer membrane, the cell wall and the inner membrane.

The goal of the first experiment was to see whether lncRNAs are differentially expressed in prostate cancer by measuring total RNA from prostate cancer cell lines and normal epithelial prostatic cells using NCode human ncRNA array and SurePrint G3 human lncRNA microarrays.

A total of 24 mice were included in the microarray expression study, four from each of the following groups: C57BL / 6J males, C57BL / 6J females, high fat — fed C57BL / 6J males, B6.Cg Ay / + females, B6.V Lepob / ob males, and B6.V Lepob / ob females.

To identify transcriptional patterns that correlate with body mass, we used oligonucleotide microarrays to catalogue gene expression levels in the parametrial or epididymal adipose tissue from two dozen mice whose body mass and adiposity varied due to diet, sex, and mutations in genes affecting energy homeostasis.

Total RNA from single animals was individually converted into biotinylated, fragmented cRNA using protocols recommended by the microarray manufacturer (Affymetrix Inc., Santa Clara, California, USA).

Samples of cRNA derived from single animals were hybridized in recommended buffer to microarrays (Murine Genome Array U74Av2, Affymetrix Inc.) at 45 °C for 16 hours.

Here, we identified genes controlling greening directly downstream of the GATAs by integrating data from RNA - sequencing and microarray data sets.

The Virochip, a pan-viral microarray containing ∼ 19,000 probes derived from all viral species in GenBank (n ∼ 2500)[21], [23], has been previously successful in detection of novel outbreak viruses such as the SARS coronavirus [22], [24] and the 2009 pandemic H1N1 influenza virus [23].

To detect novel changes in gene expression, we used a focused microarray platform to evaluate the expression profile of retinas from hypoxic animals compared to that in retinas isolated from control animals exposed to room air.

Related research (Pereira HJ, et al., 2012) used two different lines of evidence to explain the increase in the ratio of anteiso — to iso - branched alkenes that was observed during the transition from early to late stationary phase in M. luteus: structural studies of a key enzyme involved in fatty acid biosynthesis in M. luteus (FabH, or ß - ketoacyl - ACP synthase III) and transcriptional (whole - genome microarray) studies of M. luteus during different growth phases.

A focused oligonucleotide microarray of 1,178 genes, qRT — PCR of selected transcripts, and western analysis of hypoxia inducible factor - 1α (HIF - 1α) were used to compare retinas from the hypoxic and recovery groups to control animals that were not made hypoxic.

Oligonucleotide probe selection and synthesis — The 1,178 genes comprising the Falk Center for Molecular Therapeutics (FCMT) Rat CNS microarray were compiled from currently available NCBI / EMBL / TIGR rat sequence databases and commercially available central nervous system (CNS) microarrays (Affymetrix, Santa Clara, CA) and provided representation from greater than 90 % of the major gene ontological categories [47].

(A) Location of the eye field (EF), PNP, and LE tissue isolated from stage 15 Xenopus embryos for microarray analysis.

Bioinformatics services include data QC, outlier detection and general data management, and data analysis from platforms including Illumina or Affymetrix microarrays, RNA - Seq, SNP arrays, Exome - sequencing, ChIP - chips and CHIP - seq.

Target preparation and microarray hybridization — Total RNA was extracted from retinal samples using RNeasy Lipid Tissue Mini Kit (Qiagen) and was the substrate for amplification and labeling using a procedure based on the Eberwine protocol [49].

As the microarray contains a diversity of genes originated from different organisms, all genes were transformed to Homo sapiens ones.

Laurence Rubin, Identitas CEO and a practicing rheumatologist at St. Michael's Hospital in Toronto, says that his company is now shifting gears from demonstrating the utility of SNP - based microarrays for analyzing forensic samples to into more of an advocacy role, introducing law enforcement agencies to the power of these genomic technologies.

AMSBIO offers a range of kits and reagents for the extraction (isolation) of high quality RNA from FFPE tissues and LCM samples that can be used not only for PCR but also microarray applications.

We work very closely with the Sequencing and Microarray Facility (SMF) and the DNA / RNA samples extracted from us can be submitted directly from our core to SMF across the hallway.

The intensity of the emitted fluorescence from a target spot on the array was detected using an Agilent G2565BA microarray scanner.

While some microarrays contain distant sites, these often are not available from the same patient.

Results: Benefiting from the recently sequenced genome of the model sulfate - reducing bacterium (SRB), Desulfovibrio vulgaris, microbiologist Weiwen Zhang and a team of scientists at Pacific Northwest National Laboratory (PNNL) are applying a suite of post-genomics technologies, including microarray, proteomic, and computational analyses, to obtain a broader understanding of D. vulgaris» metabolism.

Patients and Methods: A tissue microarray (TMA) consisting of four biopsy cores from 34 matched pairs of nephrectomy and metastatic sites of clear cell RCC was used to assess PD - L1 expression by quantitative immunofluorescence.

In addition, analysis of the microarray results obtained with RNA from the optimized protocol showed that, as expected, the genes involved in methane production (methanogenesis) were among the most highly expressed genes in M. barkeri.

Tissue microarrays are used to show antibody staining in samples from 144 individuals corresponding to 44 different normal tissue types, and samples from 216 cancer patients corresponding to 20 different types of cancer (movie about tissue microarray production and immunohistochemical staining).

Under the stewardship of Christine Armour, the working group, consisting of members from the CCMG Clinical Practice and Laboratory Practice committees with representatives from the SOGC, have updated the 2001 Canadian guidelines for use of chromosomal microarray analysis (CMA).

Data Analysis (External Data — generated from other sources, i.e. genomics, RPPA, microarray, sequencing, etc)

Research on vaccine biomarkers, including in - depth comparative analysis of data from different platforms, large - scale RNA sequencing, harmonisation of standard operating procedures (SOPs) for sample, microarray and data analysis, as well as transcriptome mapping (more than 1400 samples analysed).

We used custom microarrays to capture and Illumina sequence 6 Mb of targeted intronic DNA, and combined this dataset with published protein coding sequences derived from transcriptome sequencing [28]--[29].

Compared with RNAseq we found that microarrays suffer from high levels of noise, possibly due to non-specific hybridization, and reach saturation with highly expressed genes [42].

To compare the expression estimates form RNAseq and microarrays to those from qRT - PCR, RNA from OM and VNO was extracted, as previously described, from four individual male and four individual female C57BL / 6J mice.

RNA was isolated from the following fractions: V −, S +; V +, S +; V −, S −; V +, S − and hybridised to a NIA Mouse 44K Microarray v2.1.

The data collected by microarray are based on the fluorescence signal intensities (analogue data) from known sequenced oligo probes.

Pollard earned a PhD in biostatistics from the University of California, Berkeley, where she developed statistical methods to analyze microarray data in cancer biology.

We obtained polymorphism and divergence data from six individuals for each of the rabbit subspecies using Illumina sequencing of genomic regions enriched by DNA hybridization on microarrays [60].