scholarly journals MicroRNA Affymetrix microarray probe labeling from ocular fluids v1 (protocols.io.bc7pizmn)

protocols.io ◽  
2020 ◽  
Author(s):  
Zeljka Smit
Keyword(s):  
Microarray Probe ◽  
Affymetrix Microarray ◽  
Ocular Fluids

scholarly journals A robust method for estimating gene expression states using Affymetrix microarray probe level data

2010 ◽  
Vol 11 (1) ◽  
Author(s):  
Megu Ohtaki ◽  
Keiko Otani ◽  
Keiko Hiyama ◽  
Naomi Kamei ◽  
Kenichi Satoh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Robust Method ◽  
Microarray Probe ◽  
Affymetrix Microarray ◽  
Level Data

scholarly journals Presence of a soluble form of acetylcholinesterase in human ocular fluids.

1991 ◽  
Vol 75 (5) ◽  
pp. 276-279 ◽  
Author(s):  
M. E. Appleyard ◽  
B. McDonald ◽  
L. Benjamin
Keyword(s):  
Soluble Form ◽  
Ocular Fluids

scholarly journals Protein oligomerization is the biochemical process highly up-regulated in porcine oocytes before in vitro maturation (IVM)

2018 ◽  
Vol 6 (4) ◽  
pp. 155-162 ◽  
Author(s):  
Sylwia Borys-Wójcik ◽  
Ievgenia Kocherova ◽  
Piotr Celichowski ◽  
Małgorzata Popis ◽  
Michal Jeseta ◽  
...  
Keyword(s):  
In Vitro Maturation ◽  
Protein Oligomerization ◽  
Dynamic Nature ◽  
Affymetrix Microarray ◽  
Expression Of Genes ◽  
Before And After ◽  
Porcine Oocyte ◽  
Lower Expression

AbstractA wide variety of mechanisms controlling oligomerization are observed. The dynamic nature of protein oligomerization is important for bioactivity control. The oocyte must undergo a series of changes to become a mature form before it can fully participate in the processes associated with its function as a female gamete. The growth of oocytes in the follicular environment is accompanied by surrounding somatic cumulus (CCs) and granulosa cells (GCs). It has been shown that oocytes tested before and after in vitro maturation (IVM) differ significantly in the transcriptomic and proteomic profiles. The aim of this study was to determine new proteomic markers for the oligomerization of porcine oocyte proteins that are associated with cell maturation competence. The Affymetrix microarray assay was performed to examine the gene expression profile associated with protein oligomerization in oocytes before and after IVM. In total, 12258 different transcriptomes were analyzed, of which 419 genes with lower expression in oocytes after IVM. We found 9 genes: GJA1, VCP, JUP, MIF, MAP3K1, INSR, ANGPTL4, EIF2AK3, DECR1, which were significantly down-regulated in oocytes after IVM (in vitro group) compared to oocytes analyzed before IVM (in vivo group). The higher expression of genes involved in the oligomerization of the protein before IVM indicates that they can be recognized as important markers of biological activation of proteins necessary for the further growth and development of pig embryos.

scholarly journals Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing

2016 ◽  
Vol 10 (1) ◽  
pp. 176-182 ◽  
Author(s):  
Reza Ranjbar ◽  
Payam Behzadi ◽  
Caterina Mammina
Keyword(s):  
Dna Microarray ◽  
Francisella Tularensis ◽  
High Specificity ◽  
Cost Effective ◽  
High Rate ◽  
Molecular Diagnostic ◽  
Microarray Technology ◽  
Microarray Probe ◽  
Specificity And Sensitivity ◽  
Oligo Microarray

Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.

scholarly journals A Tool to Build Up-To-Date Gene Annotations for Affymetrix Microarrays

2017 ◽  
Vol 3 (2) ◽  
pp. 38 ◽  
Author(s):  
Vladislava Milchevskaya ◽  
Grischa Tödt ◽  
Toby James Gibson
Keyword(s):  
Statistical Power ◽  
Gene Annotation ◽  
Clinical Diagnostics ◽  
Specific Gene ◽  
Microarray Probe ◽  
New Genes ◽  
Affymetrix Microarrays ◽  
Genome Wide ◽  
Definition Of ◽  
Genome Annotations

Genome-wide expression profiling and genotyping is widely applied in functional genomics research, ranging from stem cell studies to cancer, in drug response studies, and in clinical diagnostics. The Affymetrix GeneChip microarrays represent the most popular platform for such assays. Nevertheless, due to rapid and continuous improvement of the knowledge about the genome, the definition of many of the genes and transcripts change, and new genes are discovered. Thus the original probe information is out-dated for a number of Affymetrix platforms, and needs to be re-defined. It has been demonstrated, that accurate probe set definition improves both coverage of the gene expression analysis and its statistical power. Therefore we developed a method that incorporates the most recent genome annotations into the annotation of the microarray probe sets, using tools from the next generation sequencing. Additionally our method allows to quickly build project specific gene annotation models, as well as for comparison of microarray to RNAseq data.

scholarly journals Analysis of probe level patterns in Affymetrix microarray data

2007 ◽  
Vol 8 (1) ◽  
pp. 146 ◽  
Author(s):  
Alexander C Cambon ◽  
Abdelnaby Khalyfa ◽  
Nigel GF Cooper ◽  
Caryn M Thompson
Keyword(s):  
Microarray Data ◽  
Affymetrix Microarray ◽  
Affymetrix Microarray Data

Mapping Affymetrix Microarray Probes to the Rat Genome via a Persistent Index

2013 ◽  
pp. 15-32
Author(s):  
Susan Fairley ◽  
John D. McClure ◽  
Neil Hanlon ◽  
Rob Irving ◽  
Martin W. McBride ◽  
...  
Keyword(s):  
Perfect Match ◽  
Affymetrix Genechip ◽  
Mapping Technique ◽  
Exact Matching ◽  
Affymetrix Microarray ◽  
Microarray Experiments ◽  
New Methods ◽  
Probe Mapping ◽  
Rat Genome

A probe mapping technique using a novel implementation of a persistent q-gram index was developed. It guarantees to find all matches that meet certain definitions. These include exact matching of the central 19 bases of 25 base probes, matching the central 19 bases with at most one or three mismatches and exact matching of any 16 bases. In comparison with BLAST and BLAT, the new methods were either significantly faster or identified matches missed by the heuristics. The 16 bp method was used to map the 342,410 perfect match probes from the Affymetrix GeneChip Rat Genome 230 2.0 Array to the genome. When compared with the mapping from Ensembl, the new mapping included over seven million novel matches, providing additional evidence for researchers wishing to further investigate the sources of signals measured in microarray experiments. The results demonstrate the practicality of the index, which could support other q-gram based algorithms.

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