• FlexGen was a spin-off from Leiden University Medical Centre and Dutch Space (part of EADS) and had proprietary technologies for laser based in-situ synthesis of oligonucleotides and other biomolecules. (wikipedia.org)
  • Synthetic biology) An example of a recent application is testing of the BRCA1 and BRCA2 breast cancer risk genes The FlexArrayer is an in-house custom oligonucleotide synthesis instrument. (wikipedia.org)
  • The FlexArrayer provides microarray and oligopool synthesis typically used by: Genomics centres and sequencing facilities Health and safety institutes & microbiology labs Technology innovators in the fields of: Surface chemistries, PNA's (Peptide nucleic acid), siRNA's (Small interfering RNA) and more Production of microarrays and FleXelect oligopools is done with the FlexArrayer (see image) using proprietary technology. (wikipedia.org)
  • Before the first oligonucleotide synthesis step the complete DNA microarray surface is covered by photolabile groups. (wikipedia.org)
  • As a Postdoctoral Research fellow, you will be included in the work on the design and synthesis of synthetic ligands and improved strategies for bioconjugation of ligands to ASOs and siRNAs. (varbi.com)
  • Most of the research will exploit methods used in general organic chemistry laboratories including: synthesis, analysis and purification strategies (Flash column chromatography, MS/NMR spectroscopies, HPLC purifications). (varbi.com)
  • organic synthesis, analysis and purification strategies of organic compounds from small molecules to bioconjugates. (varbi.com)
  • Secondly, experience from peptide- and oligonucleotide synthesis using automated solid phase approaches are desired. (varbi.com)
  • Analysis of custom genomic regions of interest (e.g. specific genes, multiple variants and/or complete pathways). (wikipedia.org)
  • The completion of the sequencing of the human genome has uncovered 32,000 to 35,000 predicted genes, offering the prospect for many more drugable targets. (ddw-online.com)
  • The sequence analysis of the 32-35,000 predicted genes indicates the there may be as many as 1,000 kinase or kinase-like genes. (ddw-online.com)
  • Analysis of gene expression can include measuring expression levels of a small set of genes to whole genome expression monitoring. (ddw-online.com)
  • Using Affymetrix microarray analysis of laser-captured, CD31-positive blood vessels we have identified 63 genes that are upregulated significantly (5-72 fold) in angiogenic blood vessels associated with human invasive ductal carcinoma (IDC) of the breast as compared with blood vessels in normal human breast. (ox.ac.uk)
  • A panel of 11 genes selected according to microarray analysis were validated and tested further in 11 cancer cell lines, resulting in 4 genes, CXCR4, CDK6, USP15 and CDH1. (iiarjournals.org)
  • Another growing area of research in the Andaloussi lab pertains to the delivery of antisense oligonucleotides (ASOs) that are used to either silence genes or induce splice switching. (varbi.com)
  • We, therefore, performed independent microarray analyses to identify target genes whose expression is dependent upon both Runx2 and CBFβ. (biomedcentral.com)
  • Common target genes, with a role in modulating bone-cell function, were confirmed using a combination of siRNA, quantitative reverse transcriptase PCR (qRT-PCR), ELISA, promoter reporter analysis, Electrophoretic Mobility Shift Assay (EMSA) and chromatin immunoprecipitation (ChIP) assays. (biomedcentral.com)
  • Therefore, the aim of the present study was to investigate the gene expression patterns following siRNA‑mediated suppression of RUNX1‑RUNX1T1 and MAPK1 in Kasumi‑1 and SKNO‑1 cells and to determine the differentially expressed genes in enriched biological pathways. (prinsesmaximacentrum.nl)
  • BeadChip microarray and gene ontology analysis revealed that RUNX1‑RUNX1T1 and MAPK1 suppression reduced the proliferation rate of the t(8;21) cells with deregulated expression of several classical positive regulator genes that are otherwise known to enhance cell proliferation. (prinsesmaximacentrum.nl)
  • We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. (mdpi.com)
  • This gene shares high sequence identity with three other gene members and is clustered with those three genes at chromosome 10p15-p14. (cancer-genetics.org)
  • More than 700 miRs have been identified and registered in humans, with each individual miR predicted to target multiple genes based on the seed sequence matches in their 3'-untranslated regions (UTRs) [ 6 ]. (biomedcentral.com)
  • Further analysis revealed that a lower AR occupancy was accompanied by a reduction in FoxA1 binding at regulatory regions of AR-dependent genes. (oncotarget.com)
  • Both p53 and AR are transcription factors and can affect the expression of a broad array of genes. (oncotarget.com)
  • Quantitative analysis of RNA on a massively parallel array (RNA-MaP) 21 , 23 starts with ssDNA sequencing libraries including an RNA polymerase promoter region, a stall sequence, and a variable region complementary to the desired RNA. (nature.com)
  • 87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
  • These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. (biomedcentral.com)
  • As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs). (biomedcentral.com)
  • Using next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. (biomedcentral.com)
  • This study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. (biomedcentral.com)
  • More specifically, antisense oligonucleotides that are useful as reagents for target validation , or as drugs, are engineered molecules that differ from natural RNA but that have a base sequence that is recognized as being complementary to a very specific mRNA sequence. (genomicglossaries.com)
  • Pharmaceutical biology antisense, antisense DNA, antisense oligonucleotides. (genomicglossaries.com)
  • Highly specific and effective gene silencing of any disease can be achieved by an accurate knowledge of the target mRNA sequence and rational design of its complementary antisense agents for the downregulation of its protein message. (genomicglossaries.com)
  • A special focus is lying on the integrative analysis of multi level biomarkers, e.g. microRNA - mRNA, integrative analysis of genomic, proteomic, metabolomic and phenotypic markers. (gene-quantification.de)
  • The extracellular sequences of RON contain several domains including an N-terminal semaphorin (sema) domain, followed by the plexin, semaphorin, integrin (PSI) domain, and four immunoglobulin, plexin, transcription factor (IPT) domains. (spandidos-publications.com)
  • After the DNA library is sequenced on the Illumina flow cell, it is enzymatically double stranded by extension of a 5′ biotinylated primer. (nature.com)
  • The rapid development of new sequencing platforms, such as Roche 454 sequencing system (Roche Diagnostics) and Illumina sequencing platforms (Illumina, Inc.) offered 1000-fold increase in throughput over the Sanger sequencing technology and supported the progressive publication of more helminth genomes [ 11 ]. (biomedcentral.com)
  • Gene expression analysis may uncover or facilitate answers to these questions as well as assist research and development and health care in several other ways. (ddw-online.com)
  • Two of the most common uses of the DNA microarrays are genetic analysis and the analysis of gene expression. (ddw-online.com)
  • This report will focus in using DNA microarrays for the analysis of gene expression or expression profiling, and how DNA chips are used for drug discovery and development. (ddw-online.com)
  • Gene expression analysis in human breast cancer associated blood vessels. (ox.ac.uk)
  • Targeted analysis of 274 cytokines and global proteomics of RCC CM revealed decreased DPP4 and EGF, as well as increased AREG, FN1 and MMP1, with consistently altered gene expression in RCC cell lines and tumors. (bvsalud.org)
  • We tested our hypothesis by examining the effects of silencing C/EBPβ, DDIT4, Trib3 or α-syn with small interfering ribonucleic acid (siRNA) on METH-induced autophagy and apoptosis in the human neuroblastoma SH-SY5Y cells. (cancerindex.org)
  • Then, functional analyses, including cellular proliferation, apoptosis and Matrigel invasion and the wound healing assay, for the specific miR were conducted. (biomedcentral.com)
  • 80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. (mdpi.com)
  • Early studies of DNA melting and reformation were carried out in aqueous solutions and yielded important information about the dependence of melting temperature (Tm) on the G+C composition and salt concentration, as well as information on the dependence of the rate of reassociation on the sequence complexity of the nucleic acid. (ddw-online.com)
  • In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. (nature.com)
  • Expression levels of miR that showed significant differences between the 2 ESCC and Het-1A cells based on the comprehensive analysis were analyzed by the quantitative reverse transcriptase (RT)-PCR method. (biomedcentral.com)
  • Specific and stable hybridization of the oligo to its cognate sequence is the desired outcome of a successful experimental protocol. (genelink.com)
  • Manipulation of the oligo sequence to increase the duplex stability or in some cases to decrease the duplex stability in certain loop structure will lead to oligos with increased affinity for the target molecule. (genelink.com)
  • By means of oligonucleotide microarray and RNA interference, we reveal that the sensitizing effect of IFN-β was possibly due to attenuation of MGMT expression via induction of the protein p53. (aacrjournals.org)
  • Examination of in a different way expression gene was carried out by Significance Analysis of Microarray. (fak-signal.com)
  • Expression analysis of miRNAs predicted to bind the 3′-UTR of GNA13 revealed that miR-31 exhibited an inverse correlation to GNA13 protein expression in breast cancer cells. (biomedcentral.com)
  • Independent transcriptomic and proteomic datasets of ccRCC tumors were used for the analysis of gene and protein expression as well as the level of the immune infiltration. (bvsalud.org)
  • Massively parallel experimental assays, particularly DNA microarrays and sequencing, have revolutionized genomics research in the last decades. (nature.com)
  • However, our data establish that siRNA depletion of Rrm2, Atf1 or Hex-B had significant anti-angiogenic effects in VEGF-stimulated ex vivo mouse aortic ring assays. (ox.ac.uk)
  • You can view Archer assays alongside IDT's xGen™ NGS portfolio to find the best next generation sequencing solution for your lab. (idtdna.com)
  • Integrated DNA Technologies acquires Archer™ next generation sequencing research assays to advance actionable scientific discoveries. (idtdna.com)
  • High-throughput sequencing-RNA affinity profiling (HiTS-RAP) 22 is conceptually similar to RNA-MaP, but uses the E. coli replication terminator protein Tus to stall the RNA polymerase after transcribing the variable section of the DNA library. (nature.com)
  • Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)
  • We investigated the mechanism of chemoresistance by analysis of microRNAs using the ovarian cancer cell line KFr13 and its PTX-resistant derivative (KFr13Tx). (nature.com)
  • The objective of this project is to develop new targeting vectors that combine properties of lipids, small molecules, and cell-penetrating/endosomolytic peptides for conjugation to ASOs, as well as to develop methods for linking technology of ligands to ASOs/siRNAs. (varbi.com)
  • FleXelect oligopools consist of custom oligonucleotides in solution and can be used for in solution target enrichment prior to next generation DNA sequencing. (wikipedia.org)
  • Practical enrichment analysis Functional enrichment analysis was utilized to determine key biological processes, which supplied clues towards the underlying molecular mechanisms connected on the ad verse results of torcetrapib. (fak-signal.com)
  • SmartBase TM modifications go beyond the traditional use of RNA bases for constructing synthetic siRNAs to specifically increase duplex stability, nuclease resistance and cell permeation. (genelink.com)
  • DNA microarrays take advantage of the major feature of the DNA double helix, the sequence complementarity of the two-paired strands, by using DNA capture probes which are the complement of the expressed target sequence (mRNA, cRNA or cDNA made from the mRNA). (ddw-online.com)
  • RNA-like oligonucleotides that are complementary to a portion of a target mRNA molecule. (genomicglossaries.com)
  • A complementary RNA sequence that binds to a naturally occurring (sense) mRNA molecule, thus blocking its translation. (genomicglossaries.com)
  • Angiogenesis Profiler Array was applied here to screen different components that mediated these results amongst tumor cells handled with CM and EBM. (fak-signal.com)
  • We demonstrated that FOXK1 was overexpressed in 16 types of solid tumor tissues via tissue multi-array (TMA). (oncotarget.com)
  • We used high throughput sequencing to analyze the transcriptional profiling of myotubes. (nih.gov)
  • METHODS: Proteomic and metabolomics analysis of conditioned media isolated from normal kidney cells as well as five ccRCC cell lines was performed using mass spectrometry, with the following ELISA validation. (bvsalud.org)
  • METHODS: Conditioned media (CM) were collected from five RCC-derived cell lines (Caki-1, 786-O, A498, KIJ265T and KIJ308T) and non-tumorous control cell line (RPTEC/TERT1) and analyzed using cytokine arrays targeting 274 cytokines in addition to global CM proteomics. (bvsalud.org)
  • They also found that the amplicons were similar in size distribution to the parent cDNA and showed sequence heterogeneity. (genomicglossaries.com)
  • Cells were obtained from patients undergoing IVF and examined using cDNA-array, RT-PCR, Western blotting and immunocytochemistry. (biomedcentral.com)
  • 1. Alternating 2'-F bases and 2'OMe bases in siRNA enhances duplex stability and are more resistant to RNase degradation. (genelink.com)
  • 5. 2'F U and C substituted siRNA are more resistant to RNase degradation. (genelink.com)
  • In addition to enhancing functional delivery to these tissues, the lab also exploits single cell RNA sequencing to accurately determine tissues distribution within organs on single cell level. (varbi.com)
  • [ 4 ] It is also important to understand that the same polypeptide sequence can produce many different patterns of interresidue or intraresidue interactions. (medscape.com)
  • 40h following initiation of differentiation, myotubes were transfected with either control siRNA or siH19. (nih.gov)
  • Thus, we engineer exosomes with enhanced delivery and targeting capacities and screen our wide array of exosome designs in disease-relevant cellular and animal models. (varbi.com)
  • Genetic analysis includes procedures for genotyping, SNP (single nucleotide polymorphism) detection, strain identification and various other procedures. (ddw-online.com)
  • Biomolecular Detection and Quantification (BDQ) is an open access, peer-reviewed international journal dedicated to championing excellence in molecular study design, measurement, data analysis and reporting. (gene-quantification.de)
  • We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. (biomedcentral.com)
  • Effective siRNA design features based on sequence requirements and suggested modified bases to impart specific desired characteristics. (genelink.com)
  • Modified siRNAs that stabilize A-U base-pair interactions can induce RNAi. (genelink.com)
  • RNA molecules which hybridize to complementary sequences in either RNA or DNA altering the function of the latter. (genomicglossaries.com)
  • However, they do not simultaneously and directly measure the affinity parameters relevant to biological function and are biased towards strongly binding sequences. (nature.com)
  • Analysis of Chromosomal translocation Validation of Single-nucleotide polymorphism or SNPs (typically after whole genome or whole exome studies) Other research and diagnostic applications (e.g. (wikipedia.org)
  • 48h later after transfection, total RNA was extracted for library preparation and RNA-seq analysis to compare trancript profiles between siCon and siH19 cells. (nih.gov)
  • A systematic review and meta-analysis of pregabalin preclinical studies. (iasp-pain.org)
  • Here, we report a systematic review and meta-analysis of preclinical studies of the commercially successful drug pregabalin. (iasp-pain.org)