RBP-eCLIP Kit

$1,993.00$2,695.00

An 8 sample kit for robust transcriptome-wide identification of your RNA-binding protein targets.

Optional Data Analysis (Sequencing NOT included).

NOTE: For optimal performance of the RBP-eCLIP kit, the user must have a validated antibody for their target. The antibody can be validated with the Eclipse Antibody Validation Kit (Click here to buy) . Alternatively, the antibody can come from ENCODE or a cited eCLIP publication. For any questions, write to our application scientists at .

Description

Product Highlights 
The eCLIP kit is a simplified and robust library preparation method to identify your RNA-binding proteins targets.
Convenient
Eliminate time-consuming prep work by ordering one kit with 30+ qualified reagents. Start immediately and generate eCLIP libraries in only 4 days.
High performance
Published method and protocol improvements increase workflow efficiency and identify true binding sites with single nucleotide resolution.
Reproducible
Kits include validated protocol and qualified reagents to ensure reproducibility for better results.
Our eCLIP library preparation kit is an optimized 4-day protocol based on Van Nostrand, Yeo et al. Nature Methods 2016 paper.
Why choose the eCLIP kit?

  • 1000-fold improved library prep efficiency vs standard iCLIP-seq
  • Increased experimental success rates, decreased wasted sequencing
  • Significantly improved signal/noise ratio identifies true in vivo targets

Each kit includes:

  • All eCLIP primers and buffers needed to process 8 samples (8 IP and 8 inputs)
  • Size selection beads
  • Quality tested transfer membrane
  • Index primers

Additional information

Weight 4 lbs
Dimensions 12 × 10 × 10 cm
Add Data Analysis (Sequencing not included)

Yes, No

Protocol

RBP-eCLIP Protocol v2.01R

RBP-eCLIP Protocol v1.01R (Discontinued Catalog #ECK001)

FAQs

What are the sequencing parameters?

Eclipse Bio’s kit is based on the single-end eCLIP variant described in:

Van Nostrand EL, Nguyen TB, et al. Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol. 2017;1648:177-200. PMID: 28766298. 

Libraries generated using the eCLIP-seq method are typically sequenced using standard SE50 or SE75 conditions on the Illumina HiSeq, NovaSeq, or NextSeq platforms. eCLIP-seq libraries are compatible with paired-end sequencing if desired by the user, however due to the small size of typical eCLIP RNA fragments (~200bp), most fragments are fully sequenced in standard single-end formats.

 

What is the recommended sequencing depth per sample?

 

Eclipse Bio’s target is 25 million reads per eCLIP-seq dataset. How deeply to sequence an eCLIP-seq dataset is a challenging balance between cost and sufficient read depth to detect true binding events. In an effort to experimentally address this question, an analysis of eCLIP-seq datasets for 150 RNA binding proteins suggested that for 90% of datasets, saturation of peak information occurred at or below 8.5 million reads (See Supplementary Fig. 11 of Van Nostrand EL, et al. A Large-Scale Binding and Functional Map of Human RNA Binding Proteins. Nature (Accepted, in press)

However, we have found that targeting 25 million reads provides better coverage for abundant, broadly binding RNA binding proteins (such as HNRNPs) while still allowing pooling of ~14 eCLIP libraries per standard Illumina HiSeq 4000 lane.

What genomes are available for analysis?

We have the following genomes available for analysis: human (hg38), mouse (mm10), rat (rn6), c. elegans (ce11). Custom species may incur an additional setup fee, including the addition of a viral genome to one of our available species. Contact us at  for more information.

What are the indices for sequencing Sample-Sheet?

i7 index name i7 bases on Sample Sheet i5 index name i5 bases bases on Sample Sheet
705 ATTCAGAA 505 AGGCGAAG
706 GAATTCGT 506 TAATCTTA
707 CTGAAGCT 507 CAGGACGT
708 TAATGCGC 508 GTACTGAC

Other Tools & Resources

UV Crosslinking Protocols

UV Crosslinking Protocol of Suspension Cells

UV Crosslinking Protocol of Adherent Cells

UV Crosslinking Protocol of Tissue

Computational Analysis
Contact us for more information about data analysis options and pricing.

Quality & Safety

Adapters SDS (US)

Buffers SDS (US)

Enzymes SDS (US)

Primers SDS (US)