• We also provide guidance on useful downstream assays, specifically quantitative real-time PCR, bulk and single-cell RNA sequencing, immunofluorescence, immunohistochemistry, fluorescence in situ hybridization, scanning and transmission electron microscopy and genetic engineering. (nature.com)
  • Bley N.: Immunofluorescence, FRAP analyses and fluorescence in situ hybridization (FISH) experiments. (forschung-sachsen-anhalt.de)
  • Using RNA fluorescence in situ hybridization (FISH) measurements of genes encoding key TFs and measured bulk population dynamics, this single-cell model predicts state-switching kinetics validated by measured clonal proliferation and commitment times. (lu.se)
  • Tubule formation and three-dimensional sprouting assays and tissue fluorescence staining were conducted to investigate angiogenesis. (thno.org)
  • In vitro permeability assays, trans-endothelial invasion assays, in vivo permeability assays and tissue fluorescence staining were conducted to examine vascular permeability. (thno.org)
  • We here present a micrometer-scale implementation of fluorescence in situ hybridization that we term μFISH. (springer.com)
  • A key milestone in ISH-based techniques was fluorescence in situ hybridization (FISH) (Bauman et al. (springer.com)
  • The expression levels of FENDRR in hypoxic pulmonary artery endothelial cells (HPAECs) were detected by using quantitative real-time polymerase chain reaction (qRT-PCR) and fluorescence in situ hybridization (FISH). (biomedcentral.com)
  • Western blot, Lactate dehydrogenase (LDH) release assay, Annexin V-FITC/PI double staining, Hoechst 33342/PI fluorescence staining and Caspase-1 activity assay were used to detect the role of FENDRR in HPAEC pyroptosis. (biomedcentral.com)
  • RNA pull down assay, luciferase reporter assay and fluorescence in situ hybridization were applied to verify the interaction between BCRC-3 and microRNAs. (biomedcentral.com)
  • Fluorescence in situ hybridization assay was performed to measure the expression of the lncRNA GAS5 in chondrocytes. (spandidos-publications.com)
  • Bioinformatic analysis, RNA-protein pull down, mass spectrometry, RNA immunoprecipitation, luciferase reporter assay and fluorescence in situ hybridization were performed to validate the HNRNPL/circFAM13B/IGF2BP1/PKM2 cascade. (biomedcentral.com)
  • Luciferase reporter assays and fluorescence in situ hybridization were used to confirm the target regulation between miR-486-6p and HAT1. (researchsquare.com)
  • Microscopy, PCR, and fluorescent in situ hybridization provided evidence of norovirus infection. (cdc.gov)
  • The regulatory mechanism of lncSNHG5 was investigated by RNA sequencing, fluorescent in situ hybridization, cellular fractionation assay, mass spectrometry, RNA pull-down, RNA immunoprecipitation, gene-specific m6A assay, chromatin immunoprecipitation, dual luciferase reporter assay and actinomycin D treatment in CAFs and NFs. (thno.org)
  • Probes labeled by nick translation can be used in many different hybridization techniques including: chromogenic in situ hybridization (CISH), fluorescent in situ hybridization (FISH), screening gene banks by colony or plaque hybridization, DNA or RNA transfer hybridization, and re-association kinetic studies. (enzolifesciences.com)
  • Immunoprecipitation assays using PXR-overexpressing HepG2 (ShP51) cells revealed that PXR interacts with not only DAZAP1 but also NEAT1_2, a long noncoding RNA included in the paraspeckle, and that the interaction between PXR and NEAT1_2 was disassociated by rifampicin. (aspetjournals.org)
  • SMAD3 binding to the let-7d promoter was confirmed by chromatin immunoprecipitation, electrophoretic mobility shift assay, luciferase assays, and reduced expression of let-7d in response to transforming growth factor-beta. (nih.gov)
  • RNA immunoprecipitation (RIP) and m6A dot blot were used to detect the m6A modification levels of FENDRR. (biomedcentral.com)
  • In addition, other experiments including RNA pull down analysis, RNA immunoprecipitation, luciferase reporter assays, and chromatin immunoprecipitation as well as validating assays conducted in vivo were applied to identify the target and regulatory mechanisms of IGBP1-AS1. (biomedcentral.com)
  • RNAscope technology is an advanced in situ hybridization assay that enables visualization of single-molecule gene expression with single-cell resolution directly in intact cells and tissues. (genomeweb.com)
  • Histopathology, in situ hybridization, and western blotting were performed on murine tissues. (molvis.org)
  • By using a novel RT in situ PCR assay, viral nucleic acid was localized to the cytoplasm of large numbers of tissue leukocytes and vascular endothelium in tissues with hemorrhage and to vessels, demonstrating acute intimal and medial necrosis. (usda.gov)
  • RNA from 10 control and 10 IPF tissues was hybridized on Agilent microRNA microarrays and results were confirmed by quantitative real-time polymerase chain reaction and in situ hybridization. (nih.gov)
  • Importantly, vaccinated animals were protected against intranasal challenge with IDV [3 x 10(5) 50% tissue culture infective dose(s) (TCID50)] D/OK (n = 6) or D/600 (n = 6), based on the absence of viral RNA in necropsied tissues (5 and 7 days postchallenge) using quantitative reverse transcription-PCR and in situ hybridization. (cdc.gov)
  • In contrast, animals that received a sham DNA vaccine (n = 12) had no detectable neutralizing antibodies against IDV, and viral RNA was readily detectable in respiratory tract tissues after intranasal challenge [3 x 10(5) TCID50] with IDV D/OK (n = 6) or D/660 (n = 6). (cdc.gov)
  • Using a TUNEL (terminal deoxynucleotidyltransferase-mediated dUTP-biotin nick end labeling) assay, we found that IDV D/OK and D/600 infections induced apoptosis in epithelial cells lining alveoli and bronchioles, as well as nonepithelial cells in lung tissues. (cdc.gov)
  • RNA in situ hybridization (ISH) is a extensively used approach for the localization of mRNA in tissues. (expressionpathology.com)
  • Bone-metastatic circRNAs were screened using circRNAs deep sequencing and validated using in situ hybridization in BC tissues with or without bone metastasis. (biomedcentral.com)
  • We assessed miR-637 expression in 98 and 16 gliomas and non-tumoral brain tissues, respectively, using in situ hybridization. (scirp.org)
  • These miRNAs which targeted β -catenin mRNA were confirmed by dual-luciferase reporter system and RNA-pulldown. (hindawi.com)
  • Anticancer effects of methyl jasmonate (MJ) were measured by flow cytometry assay, western blot and qRT-PCR. (biomedcentral.com)
  • Cell proliferation was monitored by MTT and soft-agar colony formation assays, cell cycle was analyzed by flow cytometry, and cell invasion was examined by transwell assay. (biomedcentral.com)
  • The roles of miR-139-5p in CRC cells with and without KRAS mutation were determined by Cell Counting Kit-8 (CCK-8), colony formation, flow cytometry and transwell assays in vitro and by tumorigenesis and metastasis assays in vivo . (thno.org)
  • We also used in vitro assays to test a possible link between our exome-derived candidate and Notch signaling. (bmj.com)
  • In practice, double and single stranded DNAs, mRNAs, and other RNAs synthesized in vitro are all used as probes. (enzolifesciences.com)
  • Bioinformatics analysis and luciferase reporter assay were used to validate interactions among hsa_circ_0046060, miR-338-3p, and G6PC2. (hindawi.com)
  • The results of luciferase reporter assay revealed that miR-338-3p and G6PC2 were the potential targets of has_circ_0046060. (hindawi.com)
  • The mechanism underlying circIKBKB-mediated activation of NF-κB/bone remodeling factors signaling and EIF4A3-induced circIKBKB were investigated using RNA pull-down, luciferase reporter, chromatin isolation by RNA purification and enzyme-linked immunosorbent assays. (biomedcentral.com)
  • Luciferase reporter assays confirmed that miR-486-5p directly targets HAT1, and cellular localization showed that miR-486-5p and HAT1 were highly expressed in the cytoplasm. (researchsquare.com)
  • Microarrays followed by bioinformatic analyses, luciferase reporter assays and Western blotting were applied for mechanistic studies. (thno.org)
  • The RNAscope 2.5 HD Duplex Assay is based on ACD's patented signal amplification and background suppression technology. (acdbio.com)
  • RNAscope Assays do not require the RNA-free environment used for traditional ISH. (acdbio.com)
  • RNAscope probes in Channel 1 and Channel 2 are compatible with this assay which utilizes HRP-based Green and AP-based Fast Red chromogens to result in a detectable green and red signal respectively. (acdbio.com)
  • The RNAscope 2.5 HD Duplex Assay can be used for simultaneous visualization of two RNA targets while maintaining single cell resolution. (acdbio.com)
  • The RNAscope 2.5 HD Duplex reagent kits are compatible with the same RNAscope probes used previously with RNAscope 2.0 2-plex assays. (acdbio.com)
  • For customers using RNAscope 2.5 HD Duplex Manual Assay for the first time, ACD's Intro Packs include species-specific control slides, control probes, the Reagent Kit, the ImmEdge hydrophobic barrier pen and the must-have accessory VectaMount™ Mounting Medium from Vecta Labs. (acdbio.com)
  • RNAscope Target Probes (Catalog or Made-to-Order C1 & C2 Probes, compatitle with the same RNAscope probes used previously with RNAscope 2.0 2-plex assays. (acdbio.com)
  • Join the ACD team for our training webinar series and learn how to perform the RNAscope Assay successfully in your lab and obtain publication quality i n situ RNA images. (acdbio.com)
  • The webinar will provide tips and tricks to perform RNAscope assay successfully in your lab. (acdbio.com)
  • We will also discuss and review the recent RNAscope assay 2.5 product developments. (acdbio.com)
  • New developments in RNAscope manual assay. (acdbio.com)
  • Bio-Techne has expanded its Advanced Cell Diagnostics-branded RNAscope technology with the release of RNA-Protein Co-Detection Assays. (genomeweb.com)
  • Automated RNAscope ISH assays are also available for Leica Systems (LS) and Ventana Systems (VS). (selectscience.net)
  • CircRNAs are newly discovered noncoding RNAs formed through the alternative splicing of premessenger RNA (mRNA). (hindawi.com)
  • Each mRNA was quantified by ribonuclease protection assay, and mRNAs encoding rSP and rITF were localized within tissue sections by hybridization in situ with 35S antisense riboprobes. (nih.gov)
  • Hybridization in situ detected extensive rSP mRNA expression in the regenerative epithelia. (nih.gov)
  • All of the stages tested with the antisense probe demonstrated the presence of folr1 mRNA, while sense probe assayed at the same stages were negative. (luc.edu)
  • Long noncoding RNAs (lncRNAs), due to their multifunction in various biological processes, have been indicated to play a crucial role in CSC renewal and stemness maintenance. (nature.com)
  • Noncoding RNAs, including circRNAs, microRNAs, and lncRNAs, have become a significant focus of research attention due to their crucial role in regulating the progression of multiple malignancies [ 5 ], including bladder cancer, gastric cancer, nasopharyngeal carcinoma, and pancreatic cancer. (hindawi.com)
  • Emerging evidence suggests that N6-methyladenosine (m6A)-modified transcripts of long noncoding RNAs (lncRNAs) are important regulators that participate in many diseases. (biomedcentral.com)
  • Long noncoding RNAs (lncRNAs) are a large class of RNA molecules ranging in length from 200 to 100,000 nt and located in the nucleus or cytoplasm (Ponting et al. (biomedcentral.com)
  • Long non-coding RNAs (lncRNAs) may act as potential markers for prognosis and progression of liver diseases and furthermore as direct targets for therapeutic purposes. (biomedcentral.com)
  • Next, the effects of miR-637 on glioma cell migration and invasion were determined by using the transwell assay. (scirp.org)
  • The levels are (1) a core gene regulatory network (GRN) architecture from transcription factor (TF) perturbation data, (2) a stochastically controlled chromatin-state gate, and (3) a single-cell proliferation model validated by experimental clonal growth and commitment kinetic assays. (lu.se)
  • The relationship between FENDRR and dynamin-related protein 1 (DRP1) was explored using bioinformatics analysis, Chromatin Isolation by RNA Purification (CHIRP), Electrophoretic mobility shift assay (EMSA) and Methylation-Specific PCR (MSP) assays. (biomedcentral.com)
  • All RNA-ISH kits contain reagents in a convenient ready-to-use (RTU) format, and chromogenic dyes are available to interrogate a single or two genes simultaneously. (selectscience.net)
  • In most cases, circRNAs usually act as a competitive endogenous RNA (ceRNA) that can absorb miRNAs to regulate the expression of targeted genes [ 9 ]. (hindawi.com)
  • Currently, a range of probes can be synthesized to locate and quantify specific short RNAs, genes, entire chromosomes, and even cells (Evanko 2007 ). (springer.com)
  • Hüttelmaier S.: Analysis of the oncogenic potential of SR-proteins by e.g. migration, invasion and proliferation assays. (forschung-sachsen-anhalt.de)
  • Methods will include cell proliferation assays, RNA-seq, in situ hybridization and gene knockdown studies. (uconn.edu)
  • The functions of circFAM13B were verified by proliferation assays, glycolysis assays, BCa cells-CD8 + T cell co-culture assays and tumorigenesis experiment among human immune reconstitution NOG mice. (biomedcentral.com)
  • The assay uses a novel and proprietary method of in situ hybridization (ISH) to visualize single RNA molecules per cell in FFPE samples mounted on slides. (acdbio.com)
  • Circular RNAs (circRNAs) are a form of noncoding and closed loop RNA molecules and play vital roles in the progression of various types of cancer in humans. (hindawi.com)
  • Many new nucleic acid-based diagnostic tools or assays have been developed that allow analysis of DNA and RNA molecules in clinical samples. (enzolifesciences.com)
  • Exosomes secreted by the umbilical cord mesenchymal stromal cells (UMSCs) and circular RNAs (circRNAs) derived from exosomes have been shown to be associated with the progression of GDM-related complications. (hindawi.com)
  • Studies report that circular RNAs (circRNAs) derived from exosomes may play a key role in GDM development. (hindawi.com)
  • High-throughput RNA sequencing and bioinformatics analysis have led to the identification of several novel circRNAs that exhibit biological characteristics and regulatory functions [ 6 , 9 ]. (hindawi.com)
  • Circular RNAs (circRNAs) are a new member of noncoding RNAs (ncRNAs) that have recently been described as key regulators of gene expression. (biomedcentral.com)
  • Circular RNAs (circRNAs), a new member of noncoding RNAs (ncRNAs), have attracted great attentions for their closed continuous loop structure and potential value in clinical work [ 9 , 10 ]. (biomedcentral.com)
  • Some circRNAs contain miRNA response elements (MREs) and function as competing endogenous RNAs (ceRNAs) to interact with miRNAs and regulate the expression of target mRNAs. (biomedcentral.com)
  • Recently, circular RNAs (circRNAs) have been reported to contribute to cancer initiation and progression. (biomedcentral.com)
  • The role of circIKBKB in inducing bone pre-metastatic niche formation and bone metastasis was determined using osteoclastogenesis, immunofluorescence and bone resorption pit assays. (biomedcentral.com)
  • The continuous flow of probes and shaping liquid on these selected cells resulted in a 120-fold reduction of the hybridization time compared with the standard protocol (3 min vs. 6 h) and efficient rinsing, thereby shortening the total FISH assay time for centromeric probes. (springer.com)
  • It relies on the sequence-specific hybridization of probes to their complementary targets in individual cells, followed by direct or indirect detection of the labelled probe. (springer.com)
  • What are the Differences Between DNA and RNA Probes? (enzolifesciences.com)
  • Gene probes are used in various blotting and in situ hybridization (ISH) techniques for the detection of nucleic acid sequences in food industry, environmental, medical, and veterinary applications to improve the specificity of the analyses. (enzolifesciences.com)
  • Molecular probes can be broadly categorized into DNA probes and RNA probes, cDNA probes, and synthetic oligonucleotide probes. (enzolifesciences.com)
  • Nucleic acid probes are either a single stranded DNA or RNA with a strong affinity towards a specific DNA or RNA target sequence. (enzolifesciences.com)
  • TRI reagent ® is a quick and convenient ready-to-use reagent useful for efficient total RNA extraction or for the simultaneous isolation of RNA, DNA and protein. (sigmaaldrich.com)
  • TRI Reagent is an improved version of the single-step total RNA isolation reagent developed by Chomczynski. (sigmaaldrich.com)
  • A single reagent that can be used for RNA, DNA and protein isolation that is free of any contamination. (sigmaaldrich.com)
  • For those customers who want to perform FFPE DNA and RNA isolation, BioChain can provide tissue section slices in tubes instead of mounting them on glass slides. (biochain.com)
  • ISH is performed without isolation of the targets from their source, i.e., in situ , and is widely used in research and diagnostics. (springer.com)
  • In contrast to Y RNAs the 4.5SH RNA is enriched in splicing speckles, suggesting that these ncRNAs modulate the association of SR-proteins within splicing speckles as well as other nuclear functions. (forschung-sachsen-anhalt.de)
  • In mammalian genomics, only a small number of transcripts encode proteins, and the vast majority are noncoding RNAs (ncRNAs), accounting for approximately 80% of the human genome. (biomedcentral.com)
  • You will learn about manual assay improvements with regards to product sensitivity, ease-of use and robustness. (acdbio.com)
  • The addition of chloroform or 1-bromo-3-chloropropane followed by centrifugation results in the separation of the mixture into three phases: an aqueous phase containing the RNA, the interphase containing DNA, and an organic phase containing proteins. (sigmaaldrich.com)
  • The codetection assays allow researchers to simultaneously examine gene expression specific to cell types and identify cellular sources of secreted proteins. (genomeweb.com)
  • SR-proteins constitute a family of RNA-binding proteins, which mainly regulate constitutive and alternative splicing. (forschung-sachsen-anhalt.de)
  • In addition to RNA recognition motifs (RRMs) the main characteristic of SR-proteins are disordered arginine and serine (RS) repeat regions. (forschung-sachsen-anhalt.de)
  • Our preliminary results suggest that SRSF1 (serine and arginine-rich splicing factor 1) and presumably other SR-proteins associate with non-coding (nc) RNAs, the highly structured 4.5SH RNA and Y RNAs. (forschung-sachsen-anhalt.de)
  • Human genomics research has often focused on RNAs that encode proteins. (biomedcentral.com)
  • RNAs that cannot encode proteins are considered useless RNAs or transcriptional noise. (biomedcentral.com)
  • We describe viral RNA shedding duration in hospitalized patients and identify patients with recurrent shedding. (stanford.edu)
  • These assays are commercially available for detection of bacterial and viral pathogens, including HIV-1, cytomegalovirus, enteric viruses, Chlamydia trachomatis, Neisseria gonorrhoeae, and Mycobacterium tuberculosis . (medscape.com)
  • The applications of this assay include study of gene co-regulation, profile gene expression in a specific cell type (identified using a cell specific marker) and map coexpression of two targets within the same cellular context based on reliable chromogenic detection of the two transcripts. (acdbio.com)
  • By analysis of patient specific alterations in circulating tumor DNA in blood samples we aim to establish blood-based assays for early detection of lung cancer, treatment monitoring, and early detection of relapse in the primary and advanced setting. (lu.se)
  • 3) Characterize the immunogenic landscape of TNBC through molecular data and in situ analyses combined with image analysis methods. (lu.se)
  • Bioinformatics support in RIP/CLIP-studies and RNA-sequencing (splicing regulation). (forschung-sachsen-anhalt.de)
  • 1) Characterize the molecular landscape in TNBC on the DNA, RNA, epigenetic and protein level, through broad high-dimensional analysis techniques and advanced bioinformatics. (lu.se)
  • DNA/RNA probe assays are faster and sensitive so that many conventional diagnostic tests for viruses and bacteria involving culturing of the organisms are being fast replaced by molecular probe assays. (enzolifesciences.com)
  • While culture tests can take days, molecular probe assays can be performed within a few hours or minutes. (enzolifesciences.com)
  • Reverse transcriptase (RT) PCR is PCR performed on RNA targets. (medscape.com)
  • This study was intended to identify the function of long non-coding RNA (lncRNA) lncARSR in NAFLD and its role in human HCC cells (HepG2) proliferation and invasion. (biomedcentral.com)
  • The expression levels of RNA of hsa_circ_0046060, mmu_circ_0002819, and miR-338-3p were determined by quantitative real-time polymerase chain reaction (RT-qPCR). (hindawi.com)
  • We used reverse transcription-polymerase chain reaction (RT-PCR) on total RNA prepared from 9 embryonic stages. (luc.edu)
  • Reverse transcription is the synthesis of a complementary DNA sequence from an RNA template using reverse transcriptase, which is an RNA-dependent DNA polymerase. (medscape.com)
  • A model of gastric ulceration in the rat has been used to determine the expression of four messenger RNAs (mRNAs) encoding peptides considered to play active parts in the healing response. (nih.gov)
  • Ulceration was caused under anaesthesia by brief application of a liquid nitrogen-filled cryoprobe to the gastric serosal surface and RNA expression was monitored over the next 10 days. (nih.gov)
  • Expression was seen in all stages assayed. (luc.edu)
  • Circular RNA (circRNA) sequencing was performed on five pairs of BCa samples, and circFAM13B (hsa_circ_0001535) was screened out because of its remarkably low expression in BCa. (biomedcentral.com)
  • Noroviruses are nonenveloped, positive-sense, single-stranded RNA viruses ≈27-35 nm in diameter ( 6 , 7 ). (cdc.gov)
  • In a study involving 28 mismatch repair-proficient tumors and 34 mismatch repair-deficient colorectal cancer samples, researchers from the Broad Institute of MIT and Harvard used single-cell transcriptomics, in situ hybridization, and GeoMx DSP to assess the mechanisms governing interactions between colorectal tumor cells and tumor-infiltrating immune cells. (scienceboard.net)
  • The researchers quantified cellular programs defined by single-cell RNA sequencing and mapped their interactions using the GeoMx Cancer Transcriptome Atlas assay across 135 regions of interest in a subset of tumors with a high number of potentially tumor-reactive T cells. (scienceboard.net)
  • It is a nonenveloped virus with a diameter around 35-40 nm, icosahedral symmetry, and a linear positive-sense RNA genome of 6.4-8.5 kb. (wikipedia.org)
  • There is considerable heterogeneity in the genome of the PRRS virus because of inherent errors common in transcription of RNA. (iastate.edu)
  • Homogenization or lysis of the tissue sample in TRI reagent ® dissolves RNA, DNA and protein. (sigmaaldrich.com)
  • Western blot analysis and in situ hybridization confirmed the presence of AND-34 RNA and protein in lens epithelial cells, particularly at the lens equator. (molvis.org)
  • However, compared to the other forms of noncoding RNA, we know very little about the precise role of circRNA in cancer. (hindawi.com)
  • Additionally, DRP1 is a downstream target gene of FENDRR, and FENDRR formed an RNA-DNA triplex with the promoter of DRP1, which led to an increase in DRP1 promoter methylation that decreased the transcriptional level of DRP1. (biomedcentral.com)
  • Emerging studies have shown that the long non‑coding RNA (lncRNA) growth arrest‑specific transcript 5 (GAS5) is involved in the pathogenesis of OA. (spandidos-publications.com)
  • Cytopathic effect and norovirus RNA were detected at each of the 5 cell passages for genogroup I and II viruses. (cdc.gov)
  • ELISA assay was used to determine the secretion of inflammatory cytokines in cell supernatants. (researchsquare.com)
  • However, these RNAs play an indispensable role in important activities such as cell proliferation, differentiation, senescence and apoptosis. (biomedcentral.com)