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17-10494 | Magna ChIRP RNA Interactome Kit -Isolation and characterization of non-coding RNA:chromatin complexes

17-10494
12 Assays  Kit capacity: 12 Chromatin Isolation by RNA Purification Assays (includes negative control probes)
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      Overview

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      Description
      Catalogue Number17-10494
      Trade Name
      • Magna ChIRP
      DescriptionMagna ChIRP RNA Interactome Kit -Isolation and characterization of non-coding RNA:chromatin complexes
      OverviewFeatures and Advantages
      • Recover non-coding RNA containing complexes using lncRNA and other types of chromatin associated RNA as targets
      • Identify sites of genomic interaction of chromatin associated RNA
      • Perform proteomic analysis of chromatin associated RNA regulatory complexes
      • Includes Streptavidin magnetic beads, plus all key buffers, enzymes, and reagents
      • All kits include a negative control probe set and a detailed protocol
      • EZ-Magna ChIRP kit includes a biotinylated TERC lncRNA positive control probe set and qPCR and RT-qPCR detection primer sets.
      • Biotinylated capture probe sets for lncRNA TERC and NEAT1 sets are also available separately


      The Magna ChIRP RNA Interactome Kit uses the ChIRP method (Chromatin Isolation by RNA Purification) to enable identification and analysis of regions of chromatin that interact with a particular chromatin-associated RNA. This novel anti-sense probe-based capture strategy uses cross-linked chromatin to allow unbiased discovery of RNA-associated DNA sequences and proteins. To perform ChIRP two pools consisting of mulitple biotinylated oligonucleotide probes complementary to the RNA of interest are used (see figure 1). These probe sets are combined with chromatin and hybridized to the chromatin-associated RNA. Complexes containing biotinylated-probes bound to the chromatin-associated RNA are then isolated using streptavidin magnetic beads. DNA or RNA can then be recovered and analyzed by quantitative PCR or next generation sequencing (ChIRP-seq). Alternatively, proteomic analysis of the recovered chromatin can be performed.

      Learn more about the ChIRP method in JOVE! (Watch Now!)

      Need help making your own ChIRP probe sets? (Use the ChIRP probe designer tool.)
      Materials Required but Not DeliveredReagents
      • Cells, stimulated or treated as needed for the experimental system
      • PBS (RNase free)
      • Glutaraldehyde solution
      • Formamide
      • Anti-sense oligo probes against chromatin associated RNA of interest. Note that pre-designed ChIRP probe sets are available for NEAT1 lncRNA (cat# 03-308) and TERC lnRNA (cat# 03-309).
      • TRIzol® Reagent (Life Technologies Cat. #15596-018)
      • Phenol: Chloroform: Isoamyl alcohol, 25:24:1, TE Buffered Saturated pH 8.0 (EMD Millipore Cat. # 6805)
      • DNA Co-Precipitant (e.g. Pellet Paint®NF Co-Precipitant, EMD Millipore Cat. # 70748-3)
      • 3M Sodium Acetate (e.g. EMD Cat. # 567422-100ML)
      • PCR purification kit (e.g. QIAGEN, Cat. # 28106)
      • miRNeasy® Mini kit (e.g. QIAGEN, Cat. # 217004)
      • Phase Lock Gel Heavy (5 PRIME, Cat. # 2302810)
      • Reagents for qRT-PCR or qPCR Analysis
      • Reagents for RNA-seq Library Construction -if performing RNA-seq analysis
      • Reagents for DNA-seq library constructionif performing DNA-seq analysis (e.g. PureGenome™ Low Input NGS Library Construction Kit, Cat. # 17-10492
      • Additional common laboratory reagents (water, 100% ethanol, chloroform etc.)


      Equipment
      • Sonicator
      • Hybridization equipment
      • Magnetic Separation Rack (e.g. Magna GrIP™ Rack; 8 well, EMD Millipore Cat. # 20-400 or PureProteome™ Magnetic Stand, EMD Millipore Cat. # LSKMAGS08 and LSKMAGS15
      • Vortex mixer
      • Rotating wheel/platform
      • Centrifuge for cell culture
      • Microcentrifuge
      • Thermomixer® (60°C capable)
      • Variable temperature water bath or incubator
      • Rotating microtube mixer
      • Real-time PCR thermal cycler
      • NanoDrop™ or spectrophotometer
      • Microfuge tubes, pipettes, tips and other common plastic disposables
      References
      Product Information
      Components
      • 10X Glycine
      • Lysis Buffer
      • Hybridization Buffer (without 15% formamide)
      • Wash Buffer
      • Proteinase K Buffer (for DNA)
      • Proteinase K Buffer (for RNA)
      • DNA Elution Buffer
      • 0.5M EDTA
      • Streptavidin Magnetic Beads
      • RNase Inhibitor
      • Protease Inhibitor Cocktail III
      • Proteinase K Solution
      • DNase I RNase free
      • DNase I Reaction Buffer
      • RNase A (20 mg/mL)
      • RNase H (10U/ µL)
      • Magna ChIRP™ Negative Control Probe Set (LacZ)
      PresentationTwo boxes containing key reagents for extraction of ChIRP ready chromatin, plus magnetic beads enzymes, buffers,and biotinlyated negative control probes to allow the performance of 12 chromatin isolation by RNA purification assays.
      Applications
      ApplicationThe Magna ChIRP RNA Interactome Kit allows analysis, and mapping of regions of chromatin interacting with chromatin-associated RNAs. Based on the ChIRP method (chromatin isolation by RNA purification), this probe-based capture assay enables discovery of RNA-associated DNA sequences and proteins.
      Key Applications
      • DNA-binding Proteins
      • RNA Detection
      • DNA Sequencing
      • Protein Determination
      • Protein Interaction Assays
      • Purification with magnetic beads
      Biological Information
      Physicochemical Information
      Dimensions
      Materials Information
      Toxicological Information
      Safety Information according to GHS
      Safety Information
      Product Usage Statements
      Usage Statement
      • Unless otherwise stated in our catalog or other company documentation accompanying the product(s), our products are intended for research use only and are not to be used for any other purpose, which includes but is not limited to, unauthorized commercial uses, in vitro diagnostic uses, ex vivo or in vivo therapeutic uses or any type of consumption or application to humans or animals.
      Storage and Shipping Information
      Storage ConditionsUpon receipt, store components at the temperatures indicated on the labels.
      Kit components are stable for 6 months from date of shipment when stored as directed.
      Packaging Information
      Material Size12 Assays
      Material PackageKit capacity: 12 Chromatin Isolation by RNA Purification Assays (includes negative control probes)
      Transport Information
      Supplemental Information
      Specifications