lncRNA Modification Analysis

Over one hundred types of chemical modifications have been identified in RNA molecules. lncRNA modification plays a role in epigenetic regulation of gene expression. CD Genomics provides a full package of services, including m1A-seq, 5mC&5hmC profiling, m6A/m6Am profiling, pseudo-seq and m6A RNA methylation analysis by MS, with solutions tailored to your needs. We can help you obtain transcriptome-wide profiling of dynamic lncRNA modifications, deepening the understanding of the function of RNA modifications.

Overview

Long non-coding RNAs (lncRNAs) are a category of non-coding transcripts displaying length between 200 nucleotides and 100 kilobases (kb). They interact with chromatin, RNA, proteins to regulate transcriptional, post-transcriptional and translational levels of gene expression in a tissue-specific manner. The lncRNAs resemble mRNAs with a CAP structure, polyadenylated tail. However, these transcripts lack conserved open reading frames. Recently, significant progress has been made in the study of lncRNA modifications, especially for the N6-methyladenosine (m6A), which is the most abundant modification of mRNAs and has also been found in lncRNAs and other non-coding RNAs (ncRNAs). Besides, chemical modifications such as 5-methylcytosine (m5C), N1-Methyladenosine (m1A) and pseudouridine (ψ) have also been detected in lncRNA molecules.

The major methods used for the identification of lncRNA modifications rely on next-generation sequencing (NGS) or mass spectrometry (MS). CD Genomics provides a range of epitranscriptomics services to comprehensively identify lncRNA modifications, not limited to m6A, m5C, m1A and ψ. Our solutions include methylated RNA immunoprecipitation sequencing (MeRIP-seq), RNA bisulfite sequencing (RNA BS-seq), methylation individual-nucleotide-resolution crosslinking and immunoprecipitation (miCLIP), pseudo-seq and m6A RNA methylation analysis by MS, all of which are executed on with advanced NGS or MS platforms. With strong expertise and experience in epitranscriptomics, we can help you achieve a transcriptome-wide profile of all dynamic lncRNA modifications or a certain type of chemical modifications. For example, m6A-seq is a method targeting m6A in transcripts and can generate huge amounts of data covering a whole transcriptome. We are dedicated to providing accurate, single-nucleotide-resolution lncRNA methylation analysis, and further deepening the understanding of RNA methylation and biology.

Features

FlexibilityTranscriptome-WideAdvanced PlatformsQuality Control
Provide one-stop, sample-to-data service, tailored to your needsTranscriptome-wide identification of lncRNA modifications such as m6A, m1A, m5C and ψ Perform validated experiments on state-of-the-art NGS and MS instruments. Quality control is executed following every procedure.
Data Analysis Workflow

Data Analysis Workflow

In-depth data analysis:

  • Peak calling, annotation
  • lncRNA modification profiling
  • Visualization of peaks
  • Peak distribution in the transcriptome
  • Motif analysis of peak sequences
  • Differential peak analysis
  • GO functional analysis and KEGG pathway analysis

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).

Reference:

  1. Dinescu S, Ignat S, Lazar A D, et al. Epitranscriptomic signatures in lncRNAs and their possible roles in cancer. Genes, 2019, 10(1): 52.

* For Research Use Only. Not for use in diagnostic procedures.


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