lncRNA Target Prediction

Many studies have found that long noncoding RNAs (lncRNAs) perform diverse functions in multiple critical biological processes. CD Genomics provides next-generation sequencing (NGS)- and mass spectrometry (MS)-based approaches for identifying lncRNA targets and determining the functions and action mechanisms of lncRNA. This service can lay the foundations for lncRNA research and reveal its implications for diseases such as cancers.

Overview

lncRNAs have gradually become a hot topic in genome research as they are easy to find, associated with gene regulatory networks, and involved in a large number of complex diseases. However, lncRNAs are poorly conserved between species, making it more difficult for clustering and annotation. Determining the functions and action mechanisms of a large number of lncRNAs is urgently needed, and target identification is the first step for functional analysis. Advanced experimental and computational technologies have developed to provide detailed insights into lncRNAs. Here we provide NGS and MS methods and specialized software for lncRNA target prediction.

The direct targets of lncRNAs may be proteins, RNA sequences or chromatin. The determination of lncRNA targets is very important for lncRNA research. We have strong expertise and experience in handling this issue. The lncRNA gene targets are often predicted through genetic context of the lncRNA locus and lncRNA sequences. Negative or positive transcriptional regulation by lncRNAs could work either in cis or in trans. we can identify the cis- and trans-regulatory target genes of lncRNAs, and construct lncRNA-gene interaction networks. For lncRNAs with differential expression patterns or potential functions, we provide methods such as RNA pull down, ChIRP (chromatin isolation by RNA purification), RIP (RNA immunoprecipitation), CLIP (Cross-linking immunoprecipitation) for screening targets of lncRNAs.

Features

Rich ExperienceGenome-WideValidated ProcessesQuality Control
Rich experience in lncRNA sequencing and bioinformatics analysis.Genome-wide identification of lncRNA targets including proteins, RNAs and DNA.Perform advanced and validated experiments on NGS and MS instruments.Quality control is executed following every procedure.
Data Analysis Workflow

Data Analysis Workflow

In-depth data analysis:

  • Cis and Trans interaction Prediction
  • lncRNA target gene GO enrichment
  • lncRNA target genes KEGG enrichment
  • RNA pull down, ChIRP, CLIP, RIP analysis
  • Prediction of lncRNA-microRNA interactions (lncRNA-associated ceRNA networkc analysis)
  • Prediction of lncRNA-protein interaction networks

Sample Requirements

(NGS platform) RNA sample (concentration ≥ 200 ng/uL, quantity ≥ 4 ug), 1.8 ≤ OD260/280 ≤ 2.2, OD260/230≥2.0, RIN ≥ 6.5, 28S:18S≥1.0. Please make sure that RNA is not significantly degraded.
(MS platform) We work with a wide range of sample types including protein solution, fresh tissue, cultured cells, blood, and microbial sample. Please feel free to contact us for sample size.

Sample Storage: The sample should be stored at -80°C. Avoid repeated freezing and thawing.

Shipping Method: When shipping the sample, it is stored in a 1.5 mL Eppendorf tube, sealed with a sealing film. Shipments are generally recommended to contain 5-10 pounds of dry ice per 24 hours.

Deliverable:

(NGS analysis) FastQ, BAM, coverage summary, QC report, GO enrichment histogram, GO terms DAG (directed acyclic hierarchical graph), and KEGG enrichment scatter plot, and other designated report.
(MS analysis) Data QC report, MS results, integrated experimental report (materials, methodologies, and bioinformatics analysis).

References:

  1. Yan B, Wang Z H, Guo J T. The research strategies for probing the function of long noncoding RNAs. Genomics, 2012, 99(2): 76-80.
  2. Xia J, Xin L, Zhu W, et al. Characterization of long non-coding RNA transcriptome in high-energy diet induced nonalcoholic steatohepatitis minipigs. Scientific reports, 2016, 6(1): 1-11.
* For Research Use Only. Not for use in diagnostic procedures.


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