---
title: "RNA-Seq"
search_description: "IGATech's RNA sequencing (RNA-Seq) services provide high-resolution insights into gene expression, transcriptomics, and cellular responses, supporting research in genomics, oncology, and drug discovery. Unlock the potential of RNA data with our advanced solutions."
published: 2025-02-20 12:27:44.959547+00:00
locale: "it"
---

# RNA-Seq

[Request a quote](https://igatechnology.com/igatech/contacts/#contact-form)

## Technologies

![NovaSeq X Plus](/media/images/Illumina_NovaSeq_XPlus_Left_561x375.width-500.png)

### NovaSeq X Plus

The NovaSeq X Plus is a powerful and scalable ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Unrivaled data quality using Illumina's proven SBS chemistry has made the NovaSeq X Plus the instrument of choice for all major genome centers and leading institutions throughout the world. Producing up to 25 billion reads \(7.5 Tbp\) per flowcell, yielding up to 120 human genomes in about 2 days at full capacity.

![PromethION](/media/images/P24.width-500.png)

### PromethION

Oxford Nanopore's technology is providing unprecedented accessibility and scalability to long-read sequencing. The technology has  proven to be a game-changer in the fields of genome assembly, pangenomics, direct RNA sequencing and metagenomics analyses. Reads can be as long as input DNA/RNA. Bacterial genomes can be assembled in a single molecule in a snap of sequencing. Repetitive elements are easily resolved and with error-correction softwares we can now achieve telomere-to-telomere genome assemblies.

![Nucleic acids extraction](/media/images/DNA_extraction.width-500.png)

### Nucleic acids extraction

DNA and RNA extraction is routinely performed at IGATech, providing support to our customers directly from raw material. Relying on automated systems and consolidated protocols we can help you in accelerating the path to analyzed data. We also work with non standard substrates, such as [plants](https://igatechnology.com/genomics-research-services/?area=plant) and [food](https://igatechnology.com/agrigenomics-solutions/). Our expertise in the isolation of high molecular weigth DNA for long-molecule sequencing applications will also be a specialized complement for [*de novo*](http://igatechnology.com/genomics-research-services/?area=plant#denovo) applications*.* Pleas [enquire](https://igatechnology.com/igatech/contacts/) to obtain further details*.*

![RNA-Seq](/media/images/RNA-Seq.width-500.png)

### RNA-Seq

NGS platforms have become the most convenient platforms to perform accurate quantification of transcripts. Moreover, relying on sequencing information, it is possible to obtain non-trivial information such as mutation in coding regions, alternative splicing with isoforms expression levels, allelic-specific expression, intron retention, etc. Also, when performing *de novo* reconstruction of a genome, RNA-Seq data will be one of the major drivers for gene prediction and modeling. See [RNA-Seq](https://igatechnology.com/genomics-research-services/plantanimal/rna-seq/) - [smallRNA-Seq](https://igatechnology.com/genomics-research-services/small-rna/)

## Features

1. Stranded libraries
2. rRNA depletion
3. Depletion of unwanted transcripts
4. UMI-tagged libraries
5. Ultra-low input
6. Full-length cDNA sequencing with Nanopore

## Supported Analyses

1. Differential expression
2. Non-coding RNA analysis
3. De novo assembly of transcripts
4. Allelic-specific expression analysis
5. SNP discovery
6. Clustering analysis

We provide full support on study design to ensure correct sequencing and bioinformatics strategies are met based on your project goals. Our expert will consult with you about your specific requirements, and will be also your point of contact for the length of your project. See [bioinformatics](https://igatechnology.com/bioinformatics-support/).

![volcano plot](/media/images/volcanoo_plot.width-1500.png)

## **One molecule, infinite tools**

**Targeted depletion of unwanted transcripts**results in a significant reduction in sequencing reads derived from cytoplasmic and mitochondrial rRNAs, globin, chloroplasts, housekeeping genes, or any other transcript species that may not be relevant to a study, for more efficient use of sequencing resources.

## Short-reads sequencing \(Illumina or Element Biosciences\)

As a part of our standard procedure we provide **strand oriented mRNA-seq** that maintain the information on which strand the original mRNA template is coming from, allowing to accurately determine gene expression from overlapping genes or to discover antisense regulators. This method intrinsically removes most of ribosomal RNA and maximize the exploitation of coverage to estimate expression levels of coding sequences.

**Total-RNASeq** is used for those experiments that requires access also to other populations of RNAs including lncRNA and circRNA \(for small RNA please refer to a dedicated [library preparation](/sequencing-services/small-rna.md)\). Ribosomal RNA is depleted using custom probe sets specifically designed for plants, bacteria, fungi or other phyla.

For difficult samples with just picograms of RNA we advocate the use of **ultra-low inputs** library preparations supporting research in areas previously hampered by quantity of starting material \(tens of cells\).

### Bioinformatics analysis

#### Standard

- **Raw reads and Quality Control Reports**: Detailed HTML reports on read quality and preprocessing steps as well as alignment metrics.
- **Gene abundance tables**for each sample with the estimated gene expression values normalized as FPKM, TPM and raw counts.
- **Bedgraph format** files for visualization in Genome Browser
- **Differential expression analysis** \(pairwise and GLM\):
  - batch effect correction
  - PCA analysis and graphical clustering \(PCA and heatmaps\)
  - List of significantly differentially expressed genes \(p-value < 0.05\)
  - MA plot and volcano plot
  - Normalized gene expression data table
  - Statistical testing results for each comparison
  - Hierarchical and k-means cluster analysis visualization

#### **Advanced**

- **Functional Analysis**:
  - Enriched terms and gene set tables for given comparisons
  - DAVID Analysis:
    - Ontological classification for each differentially expressed gene
    - Enrichment of specific biological/functional GO terms
  - GSEA Analysis \(human and mouse only\)

- **Isoform analysis**
  - Differential Exon Usage \(DEU\)
  - Differential Transcript Usage \(DTU\)
  - Event-based Differential Splicing
  - Post-processing & Quality Control: Sorting, indexing and coverage file generation.
  - Genome browser visualization and splicing event plots

- **Variant calling**
  - SNPs and small INDELS

- **PPI network analysis from DEG list**
  - Seek potential interactions between DEGs and visualization as interaction map

## Long-reads sequencing \(Oxford Nanopore\)

**Full-length cDNA** \(Oxford Nanopore\) is used in the context of projects where full length transcripts are sequenced to obtain fine structure of isoforms and to study their differential expression or to fine annotate *de novo* assembled genomes.
**Direct RNA Sequencing:** direct RNA sequencing, powered by Oxford Nanopore Technologies provides a direct window into the viral genetic material, bypassing traditional limitations and offering a comprehensive view of viral evolution, mutation rates, and pathogenicity mechanisms. Ideal for emerging pathogens and rapidly mutating viruses this technology also allow to detect base modifications on the RNA molecule such as N6-methyladenosine \(m6A\) and pseudouridine \( Ψ \) which are now to play important role in stability of the molecule and replication rate. These same modifications are crucial for the development of RNA-based vaccines.

## Need more details?

[Talk with one of our expert!](/igatech/contacts.md)

![DSC\_0035](/media/images/DSC_0035.width-1500.jpg)

## Documents & Reports

- [Privacy Information.pdf](/documents/12/Privacy_Information_rev00.pdf)
- [Human samples clearance.pdf](/documents/13/__Human-samples_clearance.pdf)
- [Shipping and Packaging Guidelines.pdf](/documents/9/SHIPPING_AND_PACKAGING_GUIDELINES.pdf)
- [rev05 Terms and Conditions.pdf](/documents/137/__M12_01_rev05_Terms_and_Conditions.pdf)