---
title: "Single-cell RNA Service"
search_description: "IGATech offers high-resolution single-cell and spatial RNA sequencing to analyze gene expression at the cellular level, ideal for research in immunology, oncology, and developmental biology. Discover cell-specific insights with our advanced sequencing services."
published: 2025-12-12 08:39:28.826059+00:00
locale: "it"
---

# Single-cell RNA Service

[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.

![AVITI Element Biosciences](/media/images/0.width-500.png)

### AVITI Element Biosciences

The AVITI System by Element Biosciences is a benchtop sequencer designed for high performance, cost efficiency, and flexibility. It features dual independent flow cells for parallel or independent operation, enabling flexibility in throughput from low to full. The system utilizes Avidity Sequencing™ technology, ensuring over 90% of reads exceed Q30 quality, with minimal errors, low duplication rates, and reduced AT/GC bias. It supports easy data conversion to FASTQ files, offers compatibility with numerous assays, and provides cost-effective sequencing. This is our ideal companion for dedicated and fast-turnaround run set-up. For more detailed information, you can visit their website directly at [https://www.elementbiosciences.com/products/aviti](https://www.elementbiosciences.com/products/aviti).

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

### Single-cell RNA-Seq

Leveraging massive single-cell partitioning and barcoding with the Chromium platform it is possible to profile trascription patterns for up to tens of thousands of cells simultaneusly, with no lower limit on cells amount. Cell sorting and library preparation are perfomed in one day. The same technology can also be used to profile the immune system V\(D\)J repertoire of T-cells.

## Features

1. Scalable analysis from hundreds to tens of thousands of cells
2. Assistance in experimental design and sample management
3. Viability QC and dead cell removal
4. Advanced Bioinformatics Support

## Services

1. 10X Genomics preparation and sequencing
2. Parse Biosciences preparation and sequencing
3. BD Rhapsody library pool sequencing
4. Custom read length lane sequencing

> Caring of your endeavors

Expert Consulting

Our application specialists will help you in choosing the best approach for your sample type and experimental needs.

In-process QC and feedback are part of our standard procedure to avoid any waste of resources.

## True resolution

For many years, the study of transcriptome dynamics has been carried with tecnologies such as RNA sequencing and microarrays, just to name a few. These techniques usually require several million of cell to yield a pool of template RNA and be subject of the measurement. This, while being an established, robust and cost-effective experimental set-up, provides an averaged sampling of all transcriptomes across a cell population.

By using stae-of-art technology such those offered by **10X Genomics** and **Parse Biosciences,** IGATech is offering the possibility to move to a new paradigm. The platform is capable of simultaneously tagging hundreds to tens of thousands cell within a single library. After sequencing, reads can be assigned to the original cell and, based on transcriptome profiles, it is possible to distinguish subpopulations, trajectory of development, states as well as to discover associated marker genes. Moreover, oligo-antibody conjugates can be used to selectively tag specific cell types, measure the abundance of certain surface proteins and precisely stratify cells based on their differentiation state.

![UMAP](/media/images/UMAP.width-1500.png)

**BD Rhapsody library sequencing**

In collaboration with BD, IGATech is now offering an expedite sequencing service for RhaposdyTM libraries prepared by end users.

Leveraging availability of two independent platforms \(NovaSeq and AVITI\), we can provide maximized quality and cost-effectivness in the sequencing of multimodal preparations \(whole trascriptome, target panels, AbSeq, SampleTag, TCR and BCR\) and any level of cell numer and multiplexing.

## Bioinformatics Support

- **Primary Analyses**: Cell counts, sequencing metrics, gene counts, mapping performances, preliminary clustering and identification of DE genes across clusters.
- **Secondary Analysis**
  - ***Preprocessing and Visualization***: custom filtering of cells and genes, feature selection, dimensional reduction, data integration \(harmony\), normalization and scaling.
  - ***Data integration and correction of batch effect***
  - ***Exploratory Analysis:*** Clustering and cell group identification - Violin plots per cluster, correlation heatmaps, most variable genes, DE across samples, preliminary \(automatic\) cell type annotation.
  - ***Manual cell type annotation***
  - ***Differential expression analysis*****:** differential expression, gene set enrichment and pathway analysis, compositional analysis.

- **Advanced Analysis**
  - ***Gene regulatory networks***
  - ***Trajectory analysis*** \(pseudo-time and velocity\).
  - ***Integrative single-cell analysis*** \(multiple dataset, public data, cell atlas, multi-omics analyses\).

## Cell-plex

When using 10X Genomics products, the basic principle is to tag different samples with specific oligo tags conjugated with non-selective antibodies and then follow standard procedure of sample preparation and sequencing. With Parse bioscience, early segregation in the split-pool barconding process allows to prepare several samples simultaneously. This brings two extremely important benefits:

- All samples are processed in the same experiments removing batch effect.
- A single preparation reagents set is used for several samples, significantly reducing costs.

If you are interested to enter into the single-cell RNA-seq resolution, we are looking forward to help you.

[Contact us](/igatech/contacts.md) and plan your experimental set-up with one of our experts.

### Selected Publications

**The Transcriptome of SH-SY5Y at Single-Cell Resolution: A CITE-Seq Data Analysis Workflow**. **Methods Protoc.** 2021, *4*\(2\), 28; [**https://doi.org/10.3390/mps4020028**](https://doi.org/10.3390/mps4020028)
**Single-Cell Gene Network Analysis and Transcriptional Landscape of MYCN-Amplified Neuroblastoma Cell Lines. Biomolecules** 2021, *11*\(2\), 177; [**https://doi.org/10.3390/biom11020177**](https://doi.org/10.3390/biom11020177)

## Terms and Conditions

- [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)