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17-10495 EZ- Magna ChIRP RNA Interactome Kit -Isolation and characterization of non-coding RNA:chromatin complexes

The EZ-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.

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17-10495
12 Assays  Kit capacity: 12 Chromatin Isolation by RNA Purification Assays (includes negative control probes, even and odd positive control TERC lncRNA probes, and control PCR primer sets)
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Overview

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Magna Grip™ Rack 8 well (Cat.# 20-400) Now Available! or similar magnetic rack.
Description
Catalogue Number17-10495
Trade Name
  • Magna ChIRP
DescriptionEZ- Magna 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)
  • Magna ChIRP™ TERC lncRNA Probe Set (Even)
  • Magna ChIRP™ TERC lncRNA Probe Set (Odd)
  • RNA Positive Control Primers (TERC Gene)
  • RNA Negative Control Primers (GAPDH Gene)
  • Magna ChIRP™ Primers, WNT-1 precursor
  • ChIP Primers, GAPDH coding D2
PresentationThree boxes containing key reagents for the extraction of ChIRP ready chromatin, plus magnetic beads, enzymes, buffers, biotinlyated negative control probes, biotinylated TERC odd and even positive control probe set and PCR primers to allow the performance of 12 chromatin isolation by RNA purification assays.
Quality LevelMQ300
Applications
ApplicationThe EZ-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, even and odd positive control TERC lncRNA probes, and control PCR primer sets)
Transport Information
Supplemental Information
Specifications
Global Trade Item Number
Catalog Number GTIN
17-10495 04055977127065

Documentation

EZ- Magna ChIRP RNA Interactome Kit -Isolation and characterization of non-coding RNA:chromatin complexes SDS

Title

Safety Data Sheet (SDS) 

References

Reference overviewPub Med ID
Long noncoding RNA BCAR4 promotes osteosarcoma progression through activating GLI2-dependent gene transcription.
Chen, F; Mo, J; Zhang, L
Tumour Biol  13403-13412  2016

Show Abstract 		27460090 27460090

Brochure

Title
Magna ChIRP™ RNA Interactome Kits
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Technical Info

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Posters

Title
Analysis of Long Noncoding RNA Chromatin Interactions by ChIRP

User Guides

Title
EZ- Magna ChIRP RNA Interactome Kit Analysis and Mapping of Chromatin: Noncoding RNA Interactions