Bulk RNAseq service

The GENOM'IC core facility offers complete support for your bulk RNAseq projects, from samples to results analysis.

We handle sequencing of the total transcriptome, targeting coding regions (polyA), or after depletion of ribosomal RNAs, or targeting small RNAs, depending on the specifics of your project. All prepared libraries are then sequenced on an Illumina NextSeq device.

Our standard offer includes:

🔹 Initial quality control of the provided RNA (quantity, integrity)

🔹 Preparation of libraries adapted to your sample type

🔹 Sequencing of libraries (single or paired-end, adjustable depth)

🔹 Quality control of the raw data generated

Each project is subject to a personalised quote, tailored to your experimental needs (type of library, depth, number of samples, etc.).

We also offer the following optional services:

First-level bioinformatic analysis including: read alignment, alignment quality control, identification of differentially expressed genes, and differential analysis between your different conditions. You can also find on this page everything about our analysis tool RADISH to get the most out of your data.

Please contact us with any request by mail: u1016-genomique@inserm.fr, or fill out the project request form directly on our home page.

Technologies

Bulk RNA sequencing: several approaches to suit your samples

Do you have an RNAseq project? We offer several strategies depending on the quality and quantity of your RNA. Here is an overview of the different options:

‘Standard’ RNAseq

Who is it for?

You have good quality RNA (RIN > 7) in sufficient quantity (> 50 ng)

What we offer:

Capture of polyA RNAs to target messenger RNAs
Ribosomal depletion to analyse the entire transcriptome, including non-coding RNAs

The most common solutions for transcriptomic studies.

Low input RNAseq

Who is it for?

You have a small amount of RNA (< 50 ng) but still want to use your sample.

What we offer:

Protocols optimised for small volumes and rare samples.

3' RNAseq: the solution for degraded RNA

Who is it for?

Your samples are of poor quality (RIN < 5) or come from FFPE sections.

What we offer:

3' RNAseq, a robust approach for degraded RNA, with an expression profile similar to DNA chips. It is also the most economical solution (low number of reads per sample).

What if you are interested in small RNAs?

We also offer library preparation for the study of small RNAs (miRNA, etc.).

Sample type	Proposed strategy	Pros
Good quality / quantity (RIN > 7 / > 50 ng)	PolyA or ribosomal depletion	Complete transcriptome
Low quantity ( < 50 ng)	Low input RNAseq	For rare samples
Degraded RNA (RIN < 5 / FFPE)	3' RNAseq	Robust results even with altered RNA
small RNA	small RNAseq	miRNA specific

RNA-Seq analysis: a tool for exploiting your data

You can explore and generate figures from your data analysed by GENOM'IC using the RADISH tool (a RNA-Seq Dashboard In SHiny).

Feel free to try it out and contact us for more information.

Here is the Github address to discover the application and get installation information:

https://github.com/GENOM-IC-Cochin/Radish

The application can be used internally at this address: http://sequencage:3200; or externally at this address http://localhost/, after installing Docker and launching the RADISH image.

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