Tumor Long RNA-seq

Inquiry

CD Genomics's tumor long RNA sequencing (RNA-seq) service enables comprehensive analysis of mRNA and long non-coding RNA, offering the opportunity to accurately quantify expression levels of individual transcript isoforms and analyze the regulation of gene expression, including transcription start site usage, alternative splicing, and polyadenylation. Our Ph.D.-level expert team provides support at every step of your project, from early consultations to and post-delivery assistance.

Overview

Long RNA-seq is a versatile transcriptome sequencing method for comprehensively detecting long RNA molecules (> 200 nt) including coding mRNAs, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in tissues and cells. This technique can accurately and effectively uncover the genome-wide picture of the gene expression. The mRNAs correspond to the genetic sequence of genes and participate in the process of protein synthesis; the lncRNAs are a numerous type of RNA molecules that function at epigenetic levels (including DNA methylation, histone methylation, chromatin remodeling) and at both transcription and post-transcription levels by regulating gene expression; circRNAs are becoming a new hotpot in the field of RNA research as they possess closely associated with human diseases, especially cancers, and may serve as potential biomarkers.

With more than 10 years of experience in transcriptomic sequencing, CD Genomics can perform tumor long RNA-seq from ultra-low amounts of RNA (30 pg) to standard input (2 ug). Non-target RNA species such as ribosomal and globin RNA are first specifically depleted, and then strand-specific libraries are generated, followed by next-generation sequencing, data preprocessing, and advanced bioinformatics analysis. Our bioinformatic experts extract meaningful results from your sample and provide you with high-quality data analysis and visualization reports. This service is dedicated to understanding the global difference in transcriptional profiles of tumor and adjacent normal tissues, so as to reveal the transcriptional regulation mechanisms underlying tumor development, metastasis, and immunity.

Features

Strand-specific libraries	Transcriptome-Wide	Bioinformatics Analysis	One-Stop Solution
This method prepares stranded-specific RNA-seq libraries that combine rRNA removal.	Profile all mRNAs, lncRNAs and circRNAs in tumor and normal samples.	Our integrated bioinformatics pipeline can be tailored to suit your project.	One-stop solution from sample QC and library construction, to sequencing and data analysis.

Project Workflow

Sample Preparation

1. Sample Preparation

Stringent sample QC,
rRNA removal.

Library Preparation

2. Library Preparation

Strand-specific and unstranded libraries can be constructed depending on the application.

Sequencing

3. Sequencing

HiSeq X10/4000;
PE50/75/100/150;
>10G clean data

Data Analysis

4. Data Analysis

Visualize and preprocess results, and perform custom bioinformatics analysis.

Bioinformatics Analysis Pipeline

In-depth data analysis:

Genome mapping
Profiling of lncRNA, circRNA and mRNA
Predict novel lncRNA, circRNA and mRNA
Detect novel and rare transcript variants
Differential expression analysis
Target gene prediction and functional analysis
GO analysis
KEGG analysis
Annotation of circRNA and lncRNA

Sample Requirements

Total RNA (concentration ≥ 1 ng/uL, quantity ≥ 20 ng) from human tumor and adjacent normal tissues

1.8 ≤ OD260/280 ≤ 2.2, OD260/230 ≥ 2.0, RIN ≥ 6.5, 28S:18S ≥ 1.0.

Please make sure that the RNA is not significantly degraded.

Sample storage: RNA can be dissolved in ethanol or RNA-free ultra-pure water and stored at -80°C. RNA should avoid repeated freezing and thawing.

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

Deliverable: FastQ, BAM, coverage summary, QC report, custom bioinformatics analysis.

References:

Li Y, Zhao J, Yu S, et al. Extracellular vesicles long RNA sequencing reveals abundant mRNA, circRNA, and lncRNA in human blood as potential biomarkers for cancer diagnosis. Clinical chemistry, 2019, 65(6): 798-808.
Rodosthenous R S, Hutchins E, Reiman R, et al. Profiling extracellular long RNA transcriptome in human plasma and extracellular vesicles for biomarker discovery. Iscience, 2020: 101182.

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